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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
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