{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"cDNA\" and technology = \"scirnaseq\"", "rows": [[69912, "SRR19155608", "SRX15222303", "SRS12956188", "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", null, "pubmed:37968389", null, "pilot tbx16 msgn1 snRNAseq  rep3", "GSM6127478", null, "tissue:Whole embryo|cell type:Whole embryo|developmental stage:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "pilot tbx16 msgn1 snRNAseq  rep3", "The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table", "Whole embryo", null, "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "GSM6127478", "GSM6127478: pilot tbx16 msgn1 snRNAseq  rep3; Danio rerio; RNA Seq", "GSM6127478", null, "1", "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:GSM6127478", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP374541", null, null, "pilot_zperturb_seq3_R1_merge.fastq.gz pilot_zperturb_seq3_R2_merge.fastq.gz", "fastq fastq", 17724367872.0, 246171776.0, "GSM6127478 r1", "0:18 1:54", "A:5193699383;C:3933174337;G:3963953274;T:4628099313;N:5441565", 18, 54, null, null, 5193699383, 3933174337, 3963953274, 4628099313, 5441565, "SRX15222303", "SRS12956188", "SRA1418000", "GEO", "Genome Sciences, University of Washington", 2, 0.0, 0.82069, 0.0, 0.53669, 1.0, 0.85005, null, 0.60805, 18, 54, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2022-05-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [69913, "SRR19155607", "SRX15222302", "SRS12956189", "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", null, "pubmed:37968389", null, "pilot tbx16 msgn1 snRNAseq  rep2", "GSM6127477", null, "tissue:Whole embryo|cell type:Whole embryo|developmental stage:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "pilot tbx16 msgn1 snRNAseq  rep2", "The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table", "Whole embryo", null, "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "GSM6127477", "GSM6127477: pilot tbx16 msgn1 snRNAseq  rep2; Danio rerio; RNA Seq", "GSM6127477", null, "1", "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:GSM6127477", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP374541", null, null, "pilot_zperturb_seq2_R1_merge.fastq.gz pilot_zperturb_seq2_R2_merge.fastq.gz", "fastq fastq", 27578863410.0, 393983763.0, "GSM6127477 r1", "0:18 1:52", "A:7395490419;C:6434606996;G:6428176826;T:7304702878;N:15886291", 18, 52, null, null, 7395490419, 6434606996, 6428176826, 7304702878, 15886291, "SRX15222302", "SRS12956189", "SRA1418000", "GEO", "Genome Sciences, University of Washington", 2, 0.0, 0.87134, 0.0, 0.5524, 1.0, 0.84624, null, 0.63031, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2022-05-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [69914, "SRR19155606", "SRX15222301", "SRS12956187", "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", null, "pubmed:37968389", null, "pilot tbx16 msgn1 snRNAseq  rep1", "GSM6127476", null, "tissue:Whole embryo|cell type:Whole embryo|developmental stage:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "pilot tbx16 msgn1 snRNAseq  rep1", "The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table", "Whole embryo", null, "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:24 hpf prim 5|strain:AB  AB/Wik|genotype:ctrl cr  tbx16 cr  tbx16 null  tbx16 null; msgn1 MO  tbx16 cr; msgn1 cr", "GSM6127476", "GSM6127476: pilot tbx16 msgn1 snRNAseq  rep1; Danio rerio; RNA Seq", "GSM6127476", null, "1", "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and 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:GSM6127476", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP374541", null, "loader:fastq load.py", "pilot_zperturb_seq1_R1_merge.fastq.gz pilot_zperturb_seq1_R2_merge.fastq.gz", "fastq fastq", 13186963090.0, 188385187.0, "GSM6127476 r1", "0:18 1:52", "A:3934188071;C:2833481811;G:2830637414;T:3582714051;N:5941743", 18, 52, null, null, 3934188071, 2833481811, 2830637414, 3582714051, 5941743, "SRX15222301", "SRS12956187", "SRA1418000", "GEO", "Genome Sciences, University of Washington", 2, 0.0, 0.81937, 0.0, 0.56475, 1.0, 0.8437, null, 0.59396, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2022-05-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:37695017", null, "Multi genotype zebrafish skin snRNAseq", "GSM7029635", null, "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\u00b0C 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\u2103 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP421311", null, "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, null, null, 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, null, 0.58473, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2023-02-07", "Larval", "Larval", "Skin", "Surface Structure"], [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.", null, "pubmed:37695017", null, "Multi genotype zebrafish skin snRNAseq", "GSM7029635", null, "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\u00b0C 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\u2103 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP421311", null, "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, null, null, 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, null, 0.58834, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2023-02-07", "Larval", "Larval", "Skin", "Surface Structure"], [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.", null, "pubmed:37695017", null, "Multi genotype zebrafish skin snRNAseq", "GSM7029635", null, "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\u00b0C 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\u2103 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP421311", null, "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, null, null, 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, null, 0.59518, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2023-02-07", "Larval", "Larval", "Skin", "Surface Structure"], [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.", null, "pubmed:37695017", null, "Multi genotype zebrafish skin snRNAseq", "GSM7029635", null, "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\u00b0C 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\u2103 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP421311", null, "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, null, null, 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, null, 0.56962, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2023-02-07", "Larval", "Larval", "Skin", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 7, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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