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7 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "cDNA" and technology = "scirnaseq"

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  • scirnaseq · 7 ✖

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experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 7 ✖

experiment.library_layout 1

  • PAIRED · 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
69912 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   pubmed:37968389   pilot tbx16 msgn1 snRNAseq rep3 GSM6127478   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 … Whole embryo   Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. Zebrafish embryos were raised in embryo media at 28.5C. cell type:Whole embryo|developmental stage: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   1 Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. GEO Accession:GSM6127478 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP374541     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     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   0.60805 18 54 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2022-05-10 Pharyngula Embryo Whole Organism All anatomical structures
69913 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   pubmed:37968389   pilot tbx16 msgn1 snRNAseq rep2 GSM6127477   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 … Whole embryo   Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. Zebrafish embryos were raised in embryo media at 28.5C. cell type:Whole embryo|developmental stage: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   1 Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. GEO Accession:GSM6127477 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP374541     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     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   0.63031 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2022-05-10 Pharyngula Embryo Whole Organism All anatomical structures
69914 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   pubmed:37968389   pilot tbx16 msgn1 snRNAseq rep1 GSM6127476   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 … Whole embryo   Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. Zebrafish embryos were raised in embryo media at 28.5C. cell type:Whole embryo|developmental stage: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   1 Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. GEO Accession:GSM6127476 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP374541   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     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   0.59396 18 52 T B sc-like readlen illumina nextseq 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2022-05-10 Pharyngula Embryo Whole Organism All anatomical structures
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");;