metadata: run_metadata: 223 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "scirnaseq"

223 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "scirnaseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
69677	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	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	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	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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	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 …	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
69786	69786	SRR19155825	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 …	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-L002.fastq.gz	fastq	8578675700.0	85786757.0	GSM6127483 r94	0:100	A:2936872944;C:1623322385;G:1731758440;T:2286368760;N:353171	100	2936872944	1623322385	1731758440	2286368760	353171	SRX15222308	SRS12956194	SRA1418000	GEO	Genome Sciences, University of Washington	1	0.77033	0.45934	0.8198	0.50512	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
69787	69787	SRR19155826	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 …	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-L003.fastq.gz	fastq	8286484500.0	82864845.0	GSM6127483 r95	0:100	A:2858675304;C:1556958189;G:1664982635;T:2205506985;N:361387	100	2858675304	1556958189	1664982635	2205506985	361387	SRX15222308	SRS12956194	SRA1418000	GEO	Genome Sciences, University of Washington	1	0.76441	0.45637	0.81826	0.50286	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
69788	69788	SRR19155827	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 …	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-L004.fastq.gz	fastq	8350734800.0	83507348.0	GSM6127483 r96	0:100	A:2882651190;C:1568227538;G:1676184768;T:2223297514;N:373790	100	2882651190	1568227538	1676184768	2223297514	373790	SRX15222308	SRS12956194	SRA1418000	GEO	Genome Sciences, University of Washington	1	0.76306	0.45493	0.81799	0.49354	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;