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7 rows where experiment.library_selection = "cDNA", technology = "scirnaseq" and tissue_curation_coarse = "Surface Structure"

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tissue_curation 2

experiment.library_source 2

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Surface Structure · 7 ✖

technology 1

  • scirnaseq · 7 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

  • cDNA · 7 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
67811 67811 SRR17312072 SRX13488771 SRS11384713 SRP352163 PRJNA791663 Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration GSE192498 Transcriptome Analysis We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3   pubmed:35169687   5 dpa GSM5747967   source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA 5 dpa Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample adult caudal fin   Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA GSM5747967 GSM5747967: 5 dpa; Danio rerio; RNA Seq GSM5747967 r1 GSM5747967 1 Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP352163   loader:fastq load.py|options: appendBCtoName RK6.fq.gz fastq 10033219500.0 100332195.0 GSM5747967 r1 0:100 A:3474987443;C:1873037986;G:1979251566;T:2705812216;N:130289 100       3474987443 1873037986 1979251566 2705812216 130289 SRX13488771 SRS11384713 SRA1347953 Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington 1 0.71399   0.43822   0.84161   0.72626   100   B   usable mapping rate illumina novaseq_era 3prime poly_a unknown sc single_cell_plate scirnaseq   United States 2021-12-22 Adult Adult Fin Surface Structure
67812 67812 SRR17312073 SRX13488770 SRS11384711 SRP352163 PRJNA791663 Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration GSE192498 Transcriptome Analysis We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3   pubmed:35169687   3 dpa GSM5747966   source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA 3 dpa Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample adult caudal fin   Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA GSM5747966 GSM5747966: 3 dpa; Danio rerio; RNA Seq GSM5747966 r1 GSM5747966 1 Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP352163   loader:fastq load.py|options: appendBCtoName RK5.fq.gz fastq 7765549400.0 77655494.0 GSM5747966 r1 0:100 A:2667279419;C:1502480624;G:1625734956;T:1969954499;N:99902 100       2667279419 1502480624 1625734956 1969954499 99902 SRX13488770 SRS11384711 SRA1347953 Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington 1 0.65628   0.27575   0.84918   0.73771   100   B   usable mapping rate illumina novaseq_era 3prime poly_a unknown sc single_cell_plate scirnaseq   United States 2021-12-22 Adult Adult Fin Surface Structure
67813 67813 SRR17312074 SRX13488769 SRS11384712 SRP352163 PRJNA791663 Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration GSE192498 Transcriptome Analysis We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3   pubmed:35169687   3 dpa pilot GSM5747965   source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA 3 dpa pilot Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample adult caudal fin   Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA GSM5747965 GSM5747965: 3 dpa pilot; Danio rerio; RNA Seq GSM5747965 r1 GSM5747965 1 Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP352163   loader:fastq load.py|options: appendBCtoName RK.1.fq.gz fastq 4869714300.0 48697143.0 GSM5747965 r1 0:100 A:1531034092;C:971890195;G:1007416432;T:1359257595;N:115986 100       1531034092 971890195 1007416432 1359257595 115986 SRX13488769 SRS11384712 SRA1347953 Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington 1 0.60845   0.32412   0.84916   0.72554   100   B   usable mapping rate illumina novaseq_era 3prime poly_a unknown sc single_cell_plate scirnaseq   United States 2021-12-22 Adult Adult Fin Surface Structure
74043 74043 SRR23360139 SRX19301395 SRS16701439 SRP421311 PRJNA932229 Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin GSE224695 Other Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins suggest hormonal control of epithelial mesenchymal signaling clarify the signaling network that governs scale papillae development and identify a critical role for the hypodermis in supporting pigment cell development. Additionally this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type eda mutant bnc2 mutant and hypothyroid were profiled with with sci RNA seq2.   pubmed:37695017   Multi genotype zebrafish skin snRNAseq GSM7029635   tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid|geo loc name:missing|collection date:missing Multi genotype zebrafish skin snRNAseq The demultiplexing barcoded processing gene counting and aggregation were performed using the processing pipeline from Cao et al. 2017 doi: 10.1126/science.aam8940. 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: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated Whole skin tissue Hypothyroid zebrafish Tgtg:nVenus v2a nfnBwprt8Tg underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf. Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and 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 were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al. 2009. cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid GSM7029635 GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq GSM7029635 r1 GSM7029635 1 Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP421311   loader:fastq load.py zskin_sciRNA_seq1_R2_merge.fastq.gz zskin_sciRNA_seq1_R1_merge.fastq.gz fastq fastq 11447467220.0 163535246.0 GSM7029635 r1 0:18 1:52 A:3502484926;C:2381891741;G:2327139583;T:3234563798;N:1387172 18 52     3502484926 2381891741 2327139583 3234563798 1387172 SRX19301395 SRS16701439 SRA1657186 Genome Sciences, University of Washington Genome Sciences, University of Washington 2 0.0 0.82847 0.0 0.51633 1.0 0.82692   0.58473 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2023-02-07 Larval Larval Skin Surface Structure
74044 74044 SRR23360140 SRX19301395 SRS16701439 SRP421311 PRJNA932229 Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin GSE224695 Other Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins suggest hormonal control of epithelial mesenchymal signaling clarify the signaling network that governs scale papillae development and identify a critical role for the hypodermis in supporting pigment cell development. Additionally this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type eda mutant bnc2 mutant and hypothyroid were profiled with with sci RNA seq2.   pubmed:37695017   Multi genotype zebrafish skin snRNAseq GSM7029635   tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid|geo loc name:missing|collection date:missing Multi genotype zebrafish skin snRNAseq The demultiplexing barcoded processing gene counting and aggregation were performed using the processing pipeline from Cao et al. 2017 doi: 10.1126/science.aam8940. 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: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated Whole skin tissue Hypothyroid zebrafish Tgtg:nVenus v2a nfnBwprt8Tg underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf. Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and 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 were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al. 2009. cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid GSM7029635 GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq GSM7029635 r1 GSM7029635 1 Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP421311   loader:fastq load.py zskin_sciRNA_seq2_R1_merge.fastq.gz zskin_sciRNA_seq2_R2_merge.fastq.gz fastq fastq 36112843060.0 515897758.0 GSM7029635 r2 0:18 1:52 A:10807852102;C:7597254398;G:7380368668;T:10325233398;N:2134494 18 52     10807852102 7597254398 7380368668 10325233398 2134494 SRX19301395 SRS16701439 SRA1657186 Genome Sciences, University of Washington Genome Sciences, University of Washington 2 0.0 0.84202 0.0 0.54094 1.0 0.8411   0.58834 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2023-02-07 Larval Larval Skin Surface Structure
74045 74045 SRR23360141 SRX19301395 SRS16701439 SRP421311 PRJNA932229 Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin GSE224695 Other Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins suggest hormonal control of epithelial mesenchymal signaling clarify the signaling network that governs scale papillae development and identify a critical role for the hypodermis in supporting pigment cell development. Additionally this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type eda mutant bnc2 mutant and hypothyroid were profiled with with sci RNA seq2.   pubmed:37695017   Multi genotype zebrafish skin snRNAseq GSM7029635   tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid|geo loc name:missing|collection date:missing Multi genotype zebrafish skin snRNAseq The demultiplexing barcoded processing gene counting and aggregation were performed using the processing pipeline from Cao et al. 2017 doi: 10.1126/science.aam8940. 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: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated Whole skin tissue Hypothyroid zebrafish Tgtg:nVenus v2a nfnBwprt8Tg underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf. Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and 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 were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al. 2009. cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid GSM7029635 GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq GSM7029635 r1 GSM7029635 1 Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP421311   loader:fastq load.py zskin_sciRNA_seq3_R2_merge.fastq.gz zskin_sciRNA_seq3_R1_merge.fastq.gz fastq fastq 23819946500.0 340284950.0 GSM7029635 r3 0:18 1:52 A:7652488300;C:4862634258;G:4789709798;T:6501533014;N:13581130 18 52     7652488300 4862634258 4789709798 6501533014 13581130 SRX19301395 SRS16701439 SRA1657186 Genome Sciences, University of Washington Genome Sciences, University of Washington 2 0.0 0.83093 0.0 0.53155 1.0 0.82986   0.59518 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2023-02-07 Larval Larval Skin Surface Structure
74046 74046 SRR23360142 SRX19301395 SRS16701439 SRP421311 PRJNA932229 Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin GSE224695 Other Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins suggest hormonal control of epithelial mesenchymal signaling clarify the signaling network that governs scale papillae development and identify a critical role for the hypodermis in supporting pigment cell development. Additionally this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type eda mutant bnc2 mutant and hypothyroid were profiled with with sci RNA seq2.   pubmed:37695017   Multi genotype zebrafish skin snRNAseq GSM7029635   tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid|geo loc name:missing|collection date:missing Multi genotype zebrafish skin snRNAseq The demultiplexing barcoded processing gene counting and aggregation were performed using the processing pipeline from Cao et al. 2017 doi: 10.1126/science.aam8940. 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: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated Whole skin tissue Hypothyroid zebrafish Tgtg:nVenus v2a nfnBwprt8Tg underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf. Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and 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 were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al. 2009. cell type:Whole skin tissue|developmental stage:9.6 SSL SP squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type eda mutant homozygous bnc2 mutant homozygous hypothryoid GSM7029635 GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq GSM7029635 r1 GSM7029635 1 Fish were staged and selected for dissection euthanized with MS 222 and processed immediately. Following removal of the head and fins skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at 80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP421311   loader:fastq load.py zskin_sciRNA_seq4_R1_merge.fastq.gz zskin_sciRNA_seq4_R2_merge.fastq.gz fastq fastq 33417347600.0 477390680.0 GSM7029635 r4 0:18 1:52 A:10992313767;C:6719060839;G:6813342549;T:8874815927;N:17814518 18 52     10992313767 6719060839 6813342549 8874815927 17814518 SRX19301395 SRS16701439 SRA1657186 Genome Sciences, University of Washington Genome Sciences, University of Washington 2 0.0 0.7972 0.0 0.51142 1.0 0.84435   0.56962 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2023-02-07 Larval Larval Skin Surface Structure

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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");;