rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
67811,SRR17312072,SRX13488771,SRS11384713,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,5 dpa,GSM5747967,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA,5 dpa,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA,GSM5747967,GSM5747967: 5 dpa; Danio rerio; RNA Seq,GSM5747967 r1,GSM5747967,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK6.fq.gz,fastq,10033219500.0,100332195.0,GSM5747967 r1,0:100,A:3474987443;C:1873037986;G:1979251566;T:2705812216;N:130289,100,,,,3474987443,1873037986,1979251566,2705812216,130289,SRX13488771,SRS11384713,SRA1347953,"Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.71399,,0.43822,,0.84161,,0.72626,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure
67812,SRR17312073,SRX13488770,SRS11384711,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,3 dpa,GSM5747966,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,3 dpa,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,GSM5747966,GSM5747966: 3 dpa; Danio rerio; RNA Seq,GSM5747966 r1,GSM5747966,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK5.fq.gz,fastq,7765549400.0,77655494.0,GSM5747966 r1,0:100,A:2667279419;C:1502480624;G:1625734956;T:1969954499;N:99902,100,,,,2667279419,1502480624,1625734956,1969954499,99902,SRX13488770,SRS11384711,SRA1347953,"Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.65628,,0.27575,,0.84918,,0.73771,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure
67813,SRR17312074,SRX13488769,SRS11384712,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,3 dpa pilot,GSM5747965,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,3 dpa pilot,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,GSM5747965,GSM5747965: 3 dpa pilot; Danio rerio; RNA Seq,GSM5747965 r1,GSM5747965,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK.1.fq.gz,fastq,4869714300.0,48697143.0,GSM5747965 r1,0:100,A:1531034092;C:971890195;G:1007416432;T:1359257595;N:115986,100,,,,1531034092,971890195,1007416432,1359257595,115986,SRX13488769,SRS11384712,SRA1347953,"Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.60845,,0.32412,,0.84916,,0.72554,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure
69677,SRR19094454,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L001.fastq.gz,fastq,68847033000.0,688470330.0,GSM6107905 r1,0:100,A:23357162980;C:13669902202;G:15661490477;T:16154844400;N:3632941,100,,,,23357162980,13669902202,15661490477,16154844400,3632941,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.7254,,0.3995,,0.84149,,0.56669,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69678,SRR19094455,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L002.fastq.gz,fastq,64445114000.0,644451140.0,GSM6107905 r2,0:100,A:21755385809;C:12837761861;G:14651336119;T:15197372623;N:3257588,100,,,,21755385809,12837761861,14651336119,15197372623,3257588,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.73455,,0.40204,,0.84153,,0.56626,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69679,SRR19094456,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L003.fastq.gz,fastq,67150909400.0,671509094.0,GSM6107905 r3,0:100,A:22732764240;C:13367603512;G:15251969605;T:15795309966;N:3262077,100,,,,22732764240,13367603512,15251969605,15795309966,3262077,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.73136,,0.39771,,0.83796,,0.45674,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69680,SRR19094457,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L004.fastq.gz,fastq,62587489000.0,625874890.0,GSM6107905 r4,0:100,A:21160446065;C:12424654958;G:14189404686;T:14810018652;N:2964639,100,,,,21160446065,12424654958,14189404686,14810018652,2964639,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.7333,,0.40195,,0.83928,,0.56242,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69693,SRR19155732,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part1-L001.fastq.gz,fastq,9504654900.0,95046549.0,GSM6127483 r1,0:100,A:3269236251;C:1823488887;G:1923030699;T:2488567098;N:331965,100,,,,3269236251,1823488887,1923030699,2488567098,331965,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77932,,0.456,,0.82077,,0.50409,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69694,SRR19155733,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part3-L002.fastq.gz,fastq,8028928800.0,80289288.0,GSM6127483 r10,0:100,A:2759535999;C:1524680089;G:1624278378;T:2120102990;N:331344,100,,,,2759535999,1524680089,1624278378,2120102990,331344,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77955,,0.45873,,0.81848,,0.50675,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69695,SRR19155734,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part3-L003.fastq.gz,fastq,7761212200.0,77612122.0,GSM6127483 r11,0:100,A:2688948978;C:1462620928;G:1562357644;T:2046943755;N:340895,100,,,,2688948978,1462620928,1562357644,2046943755,340895,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77683,,0.45932,,0.82122,,0.50551,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69696,SRR19155735,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part3-L004.fastq.gz,fastq,7818788300.0,78187883.0,GSM6127483 r12,0:100,A:2710591219;C:1472629959;G:1572332337;T:2062881445;N:353340,100,,,,2710591219,1472629959,1572332337,2062881445,353340,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77581,,0.45743,,0.81858,,0.50651,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69697,SRR19155736,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part1-L001.fastq.gz,fastq,8677521200.0,86775212.0,GSM6127483 r13,0:100,A:3001182398;C:1650845100;G:1747702021;T:2277489351;N:302330,100,,,,3001182398,1650845100,1747702021,2277489351,302330,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77731,,0.45744,,0.82205,,0.50398,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69698,SRR19155737,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part1-L002.fastq.gz,fastq,8864501600.0,88645016.0,GSM6127483 r14,0:100,A:3053083680;C:1692148229;G:1788721364;T:2330182158;N:366169,100,,,,3053083680,1692148229,1788721364,2330182158,366169,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77893,,0.45768,,0.82276,,0.50641,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69699,SRR19155738,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part1-L003.fastq.gz,fastq,8565380600.0,85653806.0,GSM6127483 r15,0:100,A:2974854683;C:1622655481;G:1719120964;T:2248377891;N:371581,100,,,,2974854683,1622655481,1719120964,2248377891,371581,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77509,,0.45747,,0.82189,,0.49955,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69700,SRR19155739,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part1-L004.fastq.gz,fastq,8631324000.0,86313240.0,GSM6127483 r16,0:100,A:2999398386;C:1634224453;G:1730691371;T:2266624823;N:384967,100,,,,2999398386,1634224453,1730691371,2266624823,384967,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77501,,0.4579,,0.82233,,0.49821,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69701,SRR19155740,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part2-L001.fastq.gz,fastq,9168886800.0,91688868.0,GSM6127483 r17,0:100,A:3188210702;C:1731363492;G:1829864181;T:2419126810;N:321615,100,,,,3188210702,1731363492,1829864181,2419126810,321615,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77734,,0.46232,,0.82217,,0.50164,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69702,SRR19155741,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part2-L002.fastq.gz,fastq,9363835600.0,93638356.0,GSM6127483 r18,0:100,A:3242684604;C:1774486529;G:1872542661;T:2473738755;N:383051,100,,,,3242684604,1774486529,1872542661,2473738755,383051,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77929,,0.46175,,0.82085,,0.51016,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69703,SRR19155742,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part2-L003.fastq.gz,fastq,9053507400.0,90535074.0,GSM6127483 r19,0:100,A:3160890123;C:1702721288;G:1800868145;T:2388630530;N:397314,100,,,,3160890123,1702721288,1800868145,2388630530,397314,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77463,,0.46066,,0.82321,,0.50614,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69704,SRR19155743,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part1-L002.fastq.gz,fastq,9712871900.0,97128719.0,GSM6127483 r2,0:100,A:3327110045;C:1869896831;G:1969125734;T:2546335619;N:403671,100,,,,3327110045,1869896831,1969125734,2546335619,403671,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78343,,0.45956,,0.82298,,0.50835,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69705,SRR19155744,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part2-L004.fastq.gz,fastq,9123162900.0,91231629.0,GSM6127483 r20,0:100,A:3187437958;C:1714631826;G:1812709765;T:2407975769;N:407582,100,,,,3187437958,1714631826,1812709765,2407975769,407582,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77334,,0.45886,,0.82108,,0.50923,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69706,SRR19155745,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part3-L001.fastq.gz,fastq,13765002900.0,137650029.0,GSM6127483 r21,0:100,A:4640536460;C:2695529233;G:2919162530;T:3509295310;N:479367,100,,,,4640536460,2695529233,2919162530,3509295310,479367,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.79026,,0.43057,,0.82836,,0.53833,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69707,SRR19155746,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part3-L002.fastq.gz,fastq,14063371800.0,140633718.0,GSM6127483 r22,0:100,A:4720981441;C:2764505161;G:2987658251;T:3589646673;N:580274,100,,,,4720981441,2764505161,2987658251,3589646673,580274,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.79403,,0.4301,,0.82627,,0.54459,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69708,SRR19155747,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part3-L003.fastq.gz,fastq,13558861000.0,135588610.0,GSM6127483 r23,0:100,A:4591985621;C:2644034538;G:2863883103;T:3458366838;N:590900,100,,,,4591985621,2644034538,2863883103,3458366838,590900,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78785,,0.42902,,0.82641,,0.53778,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69709,SRR19155748,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.2.fq.part3-L004.fastq.gz,fastq,13662737200.0,136627372.0,GSM6127483 r24,0:100,A:4630573897;C:2661986352;G:2883559129;T:3486009792;N:608030,100,,,,4630573897,2661986352,2883559129,3486009792,608030,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78743,,0.429,,0.82686,,0.54118,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69710,SRR19155749,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part1-L001.fastq.gz,fastq,8871535200.0,88715352.0,GSM6127483 r25,0:100,A:3050449500;C:1694523268;G:1792633948;T:2333618443;N:310041,100,,,,3050449500,1694523268,1792633948,2333618443,310041,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78488,,0.4695,,0.82335,,0.50702,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69711,SRR19155750,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part1-L002.fastq.gz,fastq,9062373900.0,90623739.0,GSM6127483 r26,0:100,A:3103281762;C:1737147348;G:1834749875;T:2386817314;N:377601,100,,,,3103281762,1737147348,1834749875,2386817314,377601,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78632,,0.46924,,0.82195,,0.51659,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69712,SRR19155751,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part1-L003.fastq.gz,fastq,8751539200.0,87515392.0,GSM6127483 r27,0:100,A:3022083112;C:1664511865;G:1762196630;T:2302366067;N:381526,100,,,,3022083112,1664511865,1762196630,2302366067,381526,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77992,,0.46625,,0.82347,,0.49319,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69713,SRR19155752,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part1-L004.fastq.gz,fastq,8816645600.0,88166456.0,GSM6127483 r28,0:100,A:3046674486;C:1675683864;G:1773460542;T:2320429400;N:397308,100,,,,3046674486,1675683864,1773460542,2320429400,397308,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78084,,0.46883,,0.82144,,0.51069,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69714,SRR19155753,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part2-L001.fastq.gz,fastq,10937288800.0,109372888.0,GSM6127483 r29,0:100,A:3752292788;C:2090426809;G:2223655658;T:2870534921;N:378624,100,,,,3752292788,2090426809,2223655658,2870534921,378624,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78087,,0.46652,,0.82313,,0.51164,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69715,SRR19155754,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part1-L003.fastq.gz,fastq,9382568800.0,93825688.0,GSM6127483 r3,0:100,A:3240663611;C:1792810308;G:1891880843;T:2456806034;N:408004,100,,,,3240663611,1792810308,1891880843,2456806034,408004,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77828,,0.45538,,0.8224,,0.50749,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69716,SRR19155755,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part2-L002.fastq.gz,fastq,11177901200.0,111779012.0,GSM6127483 r30,0:100,A:3819097731;C:2144122063;G:2277194953;T:2937025866;N:460587,100,,,,3819097731,2144122063,2277194953,2937025866,460587,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78238,,0.46685,,0.82181,,0.51199,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69717,SRR19155756,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part2-L003.fastq.gz,fastq,10790009600.0,107900096.0,GSM6127483 r31,0:100,A:3717391135;C:2053700490;G:2186328727;T:2832121625;N:467623,100,,,,3717391135,2053700490,2186328727,2832121625,467623,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77841,,0.46891,,0.82292,,0.50669,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69718,SRR19155757,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part2-L004.fastq.gz,fastq,10870023700.0,108700237.0,GSM6127483 r32,0:100,A:3747371126;C:2067711014;G:2200286446;T:2854169446;N:485668,100,,,,3747371126,2067711014,2200286446,2854169446,485668,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77726,,0.46754,,0.82319,,0.51215,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69719,SRR19155758,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part3-L001.fastq.gz,fastq,9065342600.0,90653426.0,GSM6127483 r33,0:100,A:3135856555;C:1713750068;G:1819522612;T:2395897892;N:315473,100,,,,3135856555,1713750068,1819522612,2395897892,315473,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77968,,0.46629,,0.81925,,0.50804,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69720,SRR19155759,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part3-L002.fastq.gz,fastq,9264242800.0,92642428.0,GSM6127483 r34,0:100,A:3191887313;C:1757374246;G:1862787779;T:2451810673;N:382789,100,,,,3191887313,1757374246,1862787779,2451810673,382789,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78135,,0.46767,,0.82156,,0.5089,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69721,SRR19155760,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part3-L003.fastq.gz,fastq,8948090200.0,89480902.0,GSM6127483 r35,0:100,A:3107832721;C:1684740647;G:1789917771;T:2365208121;N:390940,100,,,,3107832721,1684740647,1789917771,2365208121,390940,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77626,,0.46521,,0.823,,0.51057,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69722,SRR19155761,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.3.fq.part3-L004.fastq.gz,fastq,9020077800.0,90200778.0,GSM6127483 r36,0:100,A:3134957131;C:1697229265;G:1802429121;T:2385062156;N:400127,100,,,,3134957131,1697229265,1802429121,2385062156,400127,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.776,,0.46456,,0.82331,,0.50498,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69723,SRR19155762,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part1-L001.fastq.gz,fastq,9973955900.0,99739559.0,GSM6127483 r37,0:100,A:3413194662;C:1895686435;G:2042145737;T:2622583838;N:345228,100,,,,3413194662,1895686435,2042145737,2622583838,345228,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.74745,,0.44811,,0.82493,,0.50245,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69724,SRR19155763,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part1-L002.fastq.gz,fastq,10193064000.0,101930640.0,GSM6127483 r38,0:100,A:3474102252;C:1944041444;G:2090777048;T:2683722300;N:420956,100,,,,3474102252,1944041444,2090777048,2683722300,420956,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.75037,,0.4508,,0.82487,,0.5085,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69725,SRR19155764,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part1-L003.fastq.gz,fastq,9842865600.0,98428656.0,GSM6127483 r39,0:100,A:3381398223;C:1863521187;G:2009231508;T:2588285256;N:429426,100,,,,3381398223,1863521187,2009231508,2588285256,429426,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.74427,,0.44817,,0.82548,,0.51282,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69726,SRR19155765,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part1-L004.fastq.gz,fastq,9453332300.0,94533323.0,GSM6127483 r4,0:100,A:3267237814;C:1805279320;G:1904050741;T:2476341494;N:422931,100,,,,3267237814,1805279320,1904050741,2476341494,422931,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77666,,0.45867,,0.82593,,0.51082,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69727,SRR19155766,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part1-L004.fastq.gz,fastq,9919553000.0,99195530.0,GSM6127483 r40,0:100,A:3410201831;C:1876765222;G:2022605098;T:2609539066;N:441783,100,,,,3410201831,1876765222,2022605098,2609539066,441783,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.74449,,0.44961,,0.82408,,0.50824,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69728,SRR19155767,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part2-L001.fastq.gz,fastq,10881085800.0,108810858.0,GSM6127483 r41,0:100,A:3767312164;C:2049705382;G:2179844957;T:2883847358;N:375939,100,,,,3767312164,2049705382,2179844957,2883847358,375939,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77125,,0.46558,,0.82,,0.50162,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69729,SRR19155768,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part2-L002.fastq.gz,fastq,11119560500.0,111195605.0,GSM6127483 r42,0:100,A:3834216714;C:2101867052;G:2231992258;T:2951028208;N:456268,100,,,,3834216714,2101867052,2231992258,2951028208,456268,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77519,,0.46671,,0.82195,,0.49999,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69730,SRR19155769,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part2-L003.fastq.gz,fastq,10742920100.0,107429201.0,GSM6127483 r43,0:100,A:3734467154;C:2015360747;G:2145190770;T:2847435144;N:466285,100,,,,3734467154,2015360747,2145190770,2847435144,466285,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77103,,0.46599,,0.82079,,0.50767,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69731,SRR19155770,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part2-L004.fastq.gz,fastq,10823996500.0,108239965.0,GSM6127483 r44,0:100,A:3765363558;C:2029158083;G:2158992440;T:2869997880;N:484539,100,,,,3765363558,2029158083,2158992440,2869997880,484539,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77004,,0.46485,,0.82187,,0.50171,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69732,SRR19155771,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part3-L001.fastq.gz,fastq,9264386700.0,92643867.0,GSM6127483 r45,0:100,A:3140780568;C:1764628410;G:1933960587;T:2424694341;N:322794,100,,,,3140780568,1764628410,1933960587,2424694341,322794,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.72862,,0.43297,,0.82643,,0.51065,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69733,SRR19155772,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part3-L002.fastq.gz,fastq,9472603100.0,94726031.0,GSM6127483 r46,0:100,A:3198909911;C:1809892216;G:1980540714;T:2482865316;N:394943,100,,,,3198909911,1809892216,1980540714,2482865316,394943,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.73187,,0.43823,,0.82641,,0.50735,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69734,SRR19155773,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part3-L003.fastq.gz,fastq,9148127100.0,91481271.0,GSM6127483 r47,0:100,A:3112979455;C:1736107941;G:1904273376;T:2394366306;N:400022,100,,,,3112979455,1736107941,1904273376,2394366306,400022,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.72413,,0.43493,,0.82891,,0.50579,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69735,SRR19155774,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.4.fq.part3-L004.fastq.gz,fastq,9220233800.0,92202338.0,GSM6127483 r48,0:100,A:3139585220;C:1748604640;G:1917292853;T:2414337111;N:413976,100,,,,3139585220,1748604640,1917292853,2414337111,413976,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.72592,,0.43678,,0.82741,,0.50669,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69736,SRR19155775,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part1-L001.fastq.gz,fastq,9763222500.0,97632225.0,GSM6127483 r49,0:100,A:3310875203;C:1915945257;G:2008383838;T:2527678575;N:339627,100,,,,3310875203,1915945257,2008383838,2527678575,339627,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.7871,,0.46686,,0.82369,,0.51841,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69737,SRR19155776,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part2-L001.fastq.gz,fastq,9990361900.0,99903619.0,GSM6127483 r5,0:100,A:3420448498;C:1908485409;G:2038837197;T:2622245908;N:344888,100,,,,3420448498,1908485409,2038837197,2622245908,344888,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.76133,,0.44976,,0.82375,,0.50621,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69738,SRR19155777,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part1-L002.fastq.gz,fastq,10026228000.0,100262280.0,GSM6127483 r50,0:100,A:3385793951;C:1974182877;G:2066771617;T:2599065202;N:414353,100,,,,3385793951,1974182877,2066771617,2599065202,414353,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78844,,0.46536,,0.82359,,0.51745,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69739,SRR19155778,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part1-L003.fastq.gz,fastq,9674181900.0,96741819.0,GSM6127483 r51,0:100,A:3295699713;C:1890404263;G:1982425276;T:2505232443;N:420205,100,,,,3295699713,1890404263,1982425276,2505232443,420205,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78412,,0.46399,,0.82266,,0.50164,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69740,SRR19155779,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part1-L004.fastq.gz,fastq,9718262000.0,97182620.0,GSM6127483 r52,0:100,A:3312740209;C:1897701719;G:1989683702;T:2517696635;N:439735,100,,,,3312740209,1897701719,1989683702,2517696635,439735,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78315,,0.46316,,0.82136,,0.51557,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69741,SRR19155780,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part2-L001.fastq.gz,fastq,9765655800.0,97656558.0,GSM6127483 r53,0:100,A:3288525426;C:1923097900;G:2031279735;T:2522415423;N:337316,100,,,,3288525426,1923097900,2031279735,2522415423,337316,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78789,,0.46469,,0.824,,0.50465,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69742,SRR19155781,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part2-L002.fastq.gz,fastq,9989453500.0,99894535.0,GSM6127483 r54,0:100,A:3349595876;C:1973895135;G:2081699504;T:2583853341;N:409644,100,,,,3349595876,1973895135,2081699504,2583853341,409644,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.79209,,0.46868,,0.82341,,0.51574,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69743,SRR19155782,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part2-L003.fastq.gz,fastq,9627091600.0,96270916.0,GSM6127483 r55,0:100,A:3256140380;C:1887668174;G:1995111031;T:2487751959;N:420056,100,,,,3256140380,1887668174,1995111031,2487751959,420056,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78665,,0.46532,,0.82582,,0.51427,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69744,SRR19155783,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part2-L004.fastq.gz,fastq,9698406200.0,96984062.0,GSM6127483 r56,0:100,A:3282873459;C:1900285910;G:2007884729;T:2506926533;N:435569,100,,,,3282873459,1900285910,2007884729,2506926533,435569,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78543,,0.46356,,0.82402,,0.51807,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69745,SRR19155784,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part3-L001.fastq.gz,fastq,8695419700.0,86954197.0,GSM6127483 r57,0:100,A:2967846531;C:1660968057;G:1778882914;T:2287418668;N:303530,100,,,,2967846531,1660968057,1778882914,2287418668,303530,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78041,,0.46782,,0.82284,,0.51204,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69746,SRR19155785,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part3-L002.fastq.gz,fastq,8888942400.0,88889424.0,GSM6127483 r58,0:100,A:3021447090;C:1704096611;G:1821821315;T:2341207003;N:370381,100,,,,3021447090,1704096611,1821821315,2341207003,370381,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78325,,0.46641,,0.8216,,0.50249,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69747,SRR19155786,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part3-L003.fastq.gz,fastq,8580912600.0,85809126.0,GSM6127483 r59,0:100,A:2940679820;C:1632344867;G:1749813873;T:2257700766;N:373274,100,,,,2940679820,1632344867,1749813873,2257700766,373274,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77895,,0.46481,,0.82229,,0.49812,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69748,SRR19155787,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part2-L002.fastq.gz,fastq,10212890200.0,102128902.0,GSM6127483 r6,0:100,A:3482663353;C:1957605793;G:2087822231;T:2684378509;N:420314,100,,,,3482663353,1957605793,2087822231,2684378509,420314,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.7628,,0.45135,,0.82294,,0.50602,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69749,SRR19155788,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.5.fq.part3-L004.fastq.gz,fastq,8648344900.0,86483449.0,GSM6127483 r60,0:100,A:2965795307;C:1644064672;G:1761624095;T:2276468890;N:391936,100,,,,2965795307,1644064672,1761624095,2276468890,391936,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77818,,0.46646,,0.82327,,0.50677,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69750,SRR19155789,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part1-L001.fastq.gz,fastq,9030187600.0,90301876.0,GSM6127483 r61,0:100,A:3109432073;C:1734323779;G:1818632799;T:2367486063;N:312886,100,,,,3109432073,1734323779,1818632799,2367486063,312886,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78135,,0.4596,,0.81953,,0.50646,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69751,SRR19155790,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part1-L002.fastq.gz,fastq,9229734300.0,92297343.0,GSM6127483 r62,0:100,A:3164899198;C:1778643840;G:1862485715;T:2423326603;N:378944,100,,,,3164899198,1778643840,1862485715,2423326603,378944,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78536,,0.46069,,0.81933,,0.50934,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69752,SRR19155791,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part1-L003.fastq.gz,fastq,8907613500.0,89076135.0,GSM6127483 r63,0:100,A:3079670073;C:1704066311;G:1787795298;T:2335693031;N:388787,100,,,,3079670073,1704066311,1787795298,2335693031,388787,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78076,,0.45988,,0.8199,,0.50387,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69753,SRR19155792,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part1-L004.fastq.gz,fastq,8978128700.0,89781287.0,GSM6127483 r64,0:100,A:3106122846;C:1716409487;G:1800373425;T:2354820936;N:402006,100,,,,3106122846,1716409487,1800373425,2354820936,402006,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78139,,0.46251,,0.82124,,0.51023,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69754,SRR19155793,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part2-L001.fastq.gz,fastq,10503591500.0,105035915.0,GSM6127483 r65,0:100,A:3590689419;C:2012947007;G:2139953707;T:2759637276;N:364091,100,,,,3590689419,2012947007,2139953707,2759637276,364091,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78016,,0.46521,,0.82294,,0.50794,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69755,SRR19155794,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part2-L002.fastq.gz,fastq,10735063100.0,107350631.0,GSM6127483 r66,0:100,A:3654454897;C:2064631585;G:2191485525;T:2824048671;N:442422,100,,,,3654454897,2064631585,2191485525,2824048671,442422,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78506,,0.46729,,0.82175,,0.51332,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69756,SRR19155795,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part2-L003.fastq.gz,fastq,10361305000.0,103613050.0,GSM6127483 r67,0:100,A:3556917972;C:1977073433;G:2103721625;T:2723139498;N:452472,100,,,,3556917972,1977073433,2103721625,2723139498,452472,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77856,,0.46323,,0.82183,,0.50714,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69757,SRR19155796,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part2-L004.fastq.gz,fastq,10436544500.0,104365445.0,GSM6127483 r68,0:100,A:3585399701;C:1989965975;G:2116804885;T:2743907614;N:466325,100,,,,3585399701,1989965975,2116804885,2743907614,466325,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77942,,0.46583,,0.82306,,0.51706,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69758,SRR19155797,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part3-L001.fastq.gz,fastq,8822588800.0,88225888.0,GSM6127483 r69,0:100,A:3068979717;C:1658385645;G:1753122932;T:2341791925;N:308581,100,,,,3068979717,1658385645,1753122932,2341791925,308581,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.775,,0.46501,,0.81929,,0.50289,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69759,SRR19155798,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part2-L003.fastq.gz,fastq,9856895100.0,98568951.0,GSM6127483 r7,0:100,A:3388299723;C:1875378558;G:2005128534;T:2587659156;N:429129,100,,,,3388299723,1875378558,2005128534,2587659156,429129,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.75895,,0.44828,,0.82298,,0.51015,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69760,SRR19155799,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part3-L002.fastq.gz,fastq,9011765100.0,90117651.0,GSM6127483 r70,0:100,A:3121892475;C:1699808795;G:1794159749;T:2395528379;N:375702,100,,,,3121892475,1699808795,1794159749,2395528379,375702,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77566,,0.46642,,0.82089,,0.49804,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69761,SRR19155800,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part3-L003.fastq.gz,fastq,8712013900.0,87120139.0,GSM6127483 r71,0:100,A:3042195949;C:1631307934;G:1725803445;T:2312328455;N:378117,100,,,,3042195949,1631307934,1725803445,2312328455,378117,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.76974,,0.46103,,0.82061,,0.49817,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69762,SRR19155801,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.6.fq.part3-L004.fastq.gz,fastq,8777837400.0,87778374.0,GSM6127483 r72,0:100,A:3066687446;C:1642705311;G:1737084745;T:2330966018;N:393880,100,,,,3066687446,1642705311,1737084745,2330966018,393880,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77129,,0.46341,,0.81998,,0.4977,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69763,SRR19155802,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part1-L001.fastq.gz,fastq,7895409500.0,78954095.0,GSM6127483 r73,0:100,A:2693436768;C:1515960488;G:1600663874;T:2085072227;N:276143,100,,,,2693436768,1515960488,1600663874,2085072227,276143,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77747,,0.46591,,0.82006,,0.50844,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69764,SRR19155803,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part1-L002.fastq.gz,fastq,8070102300.0,80701023.0,GSM6127483 r74,0:100,A:2741915816;C:1554844793;G:1639171868;T:2133834622;N:335201,100,,,,2741915816,1554844793,1639171868,2133834622,335201,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78155,,0.46706,,0.81921,,0.51,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69765,SRR19155804,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part1-L003.fastq.gz,fastq,7789933600.0,77899336.0,GSM6127483 r75,0:100,A:2668345284;C:1489766372;G:1573893217;T:2057588113;N:340614,100,,,,2668345284,1489766372,1573893217,2057588113,340614,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77672,,0.46954,,0.82323,,0.51461,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69766,SRR19155805,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part1-L004.fastq.gz,fastq,7848856000.0,78488560.0,GSM6127483 r76,0:100,A:2690617573;C:1499944655;G:1584064347;T:2073879159;N:350266,100,,,,2690617573,1499944655,1584064347,2073879159,350266,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77515,,0.46599,,0.81911,,0.5213,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69767,SRR19155806,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part2-L001.fastq.gz,fastq,9184533500.0,91845335.0,GSM6127483 r77,0:100,A:3165453428;C:1744434079;G:1840384244;T:2433943692;N:318057,100,,,,3165453428,1744434079,1840384244,2433943692,318057,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.7741,,0.46314,,0.81884,,0.5097,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69768,SRR19155807,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part2-L002.fastq.gz,fastq,9387284300.0,93872843.0,GSM6127483 r78,0:100,A:3222641222;C:1788869339;G:1884569932;T:2490818601;N:385206,100,,,,3222641222,1788869339,1884569932,2490818601,385206,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77665,,0.46398,,0.82002,,0.509,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69769,SRR19155808,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part2-L003.fastq.gz,fastq,9063548500.0,90635485.0,GSM6127483 r79,0:100,A:3136114717;C:1714857357;G:1810429891;T:2401753047;N:393488,100,,,,3136114717,1714857357,1810429891,2401753047,393488,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77285,,0.46292,,0.81957,,0.50557,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69770,SRR19155809,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part2-L004.fastq.gz,fastq,9933734200.0,99337342.0,GSM6127483 r8,0:100,A:3416726725;C:1888920289;G:2018621130;T:2609022226;N:443830,100,,,,3416726725,1888920289,2018621130,2609022226,443830,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.75799,,0.44863,,0.82144,,0.50712,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69771,SRR19155810,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part2-L004.fastq.gz,fastq,9133173000.0,91331730.0,GSM6127483 r80,0:100,A:3162372053;C:1726849171;G:1822337934;T:2421203694;N:410148,100,,,,3162372053,1726849171,1822337934,2421203694,410148,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77104,,0.46183,,0.82008,,0.50628,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69772,SRR19155811,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part3-L001.fastq.gz,fastq,8956701500.0,89567015.0,GSM6127483 r81,0:100,A:3082282190;C:1714389910;G:1804862002;T:2354853510;N:313888,100,,,,3082282190,1714389910,1804862002,2354853510,313888,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.7814,,0.46692,,0.82037,,0.51468,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69773,SRR19155812,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part3-L002.fastq.gz,fastq,9159219300.0,91592193.0,GSM6127483 r82,0:100,A:3139184861;C:1759232296;G:1849589197;T:2410834227;N:378719,100,,,,3139184861,1759232296,1849589197,2410834227,378719,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78609,,0.46747,,0.81998,,0.51484,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69774,SRR19155813,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part3-L003.fastq.gz,fastq,8834065900.0,88340659.0,GSM6127483 r83,0:100,A:3052744354;C:1684229126;G:1774100023;T:2322606451;N:385946,100,,,,3052744354,1684229126,1774100023,2322606451,385946,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77978,,0.46464,,0.81992,,0.51307,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69775,SRR19155814,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.7.fq.part3-L004.fastq.gz,fastq,8904450300.0,89044503.0,GSM6127483 r84,0:100,A:3079295570;C:1696361727;G:1786451296;T:2341944781;N:396926,100,,,,3079295570,1696361727,1786451296,2341944781,396926,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77956,,0.46704,,0.81844,,0.51068,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69776,SRR19155815,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part1-L001.fastq.gz,fastq,9792967100.0,97929671.0,GSM6127483 r85,0:100,A:3324790897;C:1890533478;G:2024032211;T:2553271230;N:339284,100,,,,3324790897,1890533478,2024032211,2553271230,339284,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78351,,0.46198,,0.82114,,0.51714,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69777,SRR19155816,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part1-L002.fastq.gz,fastq,10016455600.0,100164556.0,GSM6127483 r86,0:100,A:3387019666;C:1940601168;G:2073787574;T:2614635784;N:411408,100,,,,3387019666,1940601168,2073787574,2614635784,411408,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78526,,0.46306,,0.82187,,0.5161,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69778,SRR19155817,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part1-L003.fastq.gz,fastq,9659868300.0,96598683.0,GSM6127483 r87,0:100,A:3293457240;C:1857421217;G:1989634532;T:2518935851;N:419460,100,,,,3293457240,1857421217,1989634532,2518935851,419460,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78269,,0.46362,,0.82353,,0.51268,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69779,SRR19155818,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part1-L004.fastq.gz,fastq,9730675500.0,97306755.0,GSM6127483 r88,0:100,A:3319796791;C:1869585932;G:2002299570;T:2538559625;N:433582,100,,,,3319796791,1869585932,2002299570,2538559625,433582,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77951,,0.4623,,0.82306,,0.51387,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69780,SRR19155819,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part2-L001.fastq.gz,fastq,10343020100.0,103430201.0,GSM6127483 r89,0:100,A:3477057542;C:2016813447;G:2168679544;T:2680108664;N:360903,100,,,,3477057542,2016813447,2168679544,2680108664,360903,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.7789,,0.45576,,0.82434,,0.51599,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69781,SRR19155820,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.1.fq.part3-L001.fastq.gz,fastq,7860942100.0,78609421.0,GSM6127483 r9,0:100,A:2712480636;C:1487615252;G:1587464717;T:2073107948;N:273547,100,,,,2712480636,1487615252,1587464717,2073107948,273547,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77825,,0.45925,,0.8199,,0.50734,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69782,SRR19155821,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part2-L002.fastq.gz,fastq,10570934600.0,105709346.0,GSM6127483 r90,0:100,A:3539105946;C:2068758567;G:2220397235;T:2742235076;N:437776,100,,,,3539105946,2068758567,2220397235,2742235076,437776,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.78,,0.45541,,0.82556,,0.51978,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69783,SRR19155822,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part2-L003.fastq.gz,fastq,10189718600.0,101897186.0,GSM6127483 r91,0:100,A:3440867169;C:1978358047;G:2128523312;T:2641525769;N:444303,100,,,,3440867169,1978358047,2128523312,2641525769,444303,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77708,,0.4543,,0.82481,,0.52365,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69784,SRR19155823,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part2-L004.fastq.gz,fastq,10267327600.0,102673276.0,GSM6127483 r92,0:100,A:3469400433;C:1991909190;G:2142634416;T:2662920575;N:462986,100,,,,3469400433,1991909190,2142634416,2662920575,462986,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.77526,,0.4551,,0.82627,,0.52056,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures
69785,SRR19155824,SRX15222308,SRS12956194,SRP374541,PRJNA836866,Embryo scale reverse genetics at single cell resolution,GSE202639,Transcriptome Analysis,The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data  however  has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos  encompassing 19 time points  23 genetic perturbations  and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types  resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons  a cell population that comprises less than 1% of the embryo. Additionally  time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells  leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution  organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types  while also addressing long standing challenges in developmental genetics  including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7  2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS,,pubmed:37968389,,Zebrafish perturbation atlas plates4 6,GSM6127483,,tissue:Whole embryo|cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,Zebrafish perturbation atlas plates4 6,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish embryos were raised in embryo media at 28.5C.,cell type:Whole embryo|developmental stage:18  24  36  48  72 hpf|strain:AB|genotype:ctrl cr  tbx16  tbx16 tbx16l  tbx16 msgn1  cdx4  cdx4 cdx1a  tbxta  tbx16  tbx16l  msgn1  wnt3a wnt8a  noto  smo  tbx1  hand2  egr2b  epha4a  hoxb1a  mafba  zc4h2  phox2a  foxi1  hgfa  met  foxd3  tfap2a  tfap2a foxd3,GSM6127483,GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq,GSM6127483,,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,GEO Accession:GSM6127483,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP374541,,,GAP16_run2.8.fq.part3-L001.fastq.gz,fastq,8397901400.0,83979014.0,GSM6127483 r93,0:100,A:2886119731;C:1583910501;G:1692374171;T:2235204730;N:292267,100,,,,2886119731,1583910501,1692374171,2235204730,292267,SRX15222308,SRS12956194,SRA1418000,GEO,"Genome Sciences, University of Washington",1,0.76854,,0.45754,,0.81736,,0.51352,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-10,Larval,Larval,Whole Organism,All anatomical structures