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
30662,SRR28125659,SRX23770350,SRS20595835,SRP492124,PRJNA1081449,Thymic mimetic cells in zebrafish,GSE259418,Transcriptome Analysis,We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells  a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically  we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067  GSM5732070  GSM5732077   GSM5732078  GSM5732079  GSM5732080  GSM5732081  GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition  we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII  whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching  filtering  and cell sorting. The live  non autofluorescent  GFP negative  mCherry negative cells a population depleted of T and B cells  thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult  Thymus  3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult  Thymus  4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult  Thymus  1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult  Thymus  2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile  Thymus  1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile  Thymus  2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile  Thymus  3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile  Thymus  4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5,,,,adult thy untreated,GSM8115869,,tissue:13 wpf wpf loc name:missing|collection date:missing,adult thy untreated,The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms,13 wpf,,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.,tissue:13 wpf,GSM8115869,GSM8115869: adult thy untreated; Danio rerio; RNA Seq,GSM8115869 r1,GSM8115869,1,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP492124,,loader:fastq load.py,adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz,fastq fastq fastq,61867658967.0,487146921.0,GSM8115869 r1,0:8 1:28 2:91,A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420,8,28,91,,12933400034,9373762639,10188374364,11834295354,537420,SRX23770350,SRS20595835,,,"Oncology/Hematology, Boston Children's Hospital",1,0.90847,,0.19603,,0.76895,,0.56494,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-27,Multi-stage,Multi-stage,Undetermined,Undetermined
30663,SRR28125660,SRX23770349,SRS20595836,SRP492124,PRJNA1081449,Thymic mimetic cells in zebrafish,GSE259418,Transcriptome Analysis,We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells  a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically  we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067  GSM5732070  GSM5732077   GSM5732078  GSM5732079  GSM5732080  GSM5732081  GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition  we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII  whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching  filtering  and cell sorting. The live  non autofluorescent  GFP negative  mCherry negative cells a population depleted of T and B cells  thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult  Thymus  3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult  Thymus  4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult  Thymus  1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult  Thymus  2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile  Thymus  1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile  Thymus  2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile  Thymus  3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile  Thymus  4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5,,,,adult thy liberase 2,GSM8115868,,tissue:13 wpf wpf loc name:missing|collection date:missing,adult thy liberase 2,The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms,13 wpf,,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.,tissue:13 wpf,GSM8115868,GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq,GSM8115868 r1,GSM8115868,1,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP492124,,loader:fastq load.py,adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz,fastq fastq fastq,64816880653.0,510369139.0,GSM8115868 r1,0:8 1:28 2:91,A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488,8,28,91,,12985717325,10400471721,10926930853,12129907262,564488,SRX23770349,SRS20595836,,,"Oncology/Hematology, Boston Children's Hospital",1,0.90014,,0.13619,,0.81103,,0.54906,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-27,Multi-stage,Multi-stage,Undetermined,Undetermined
30664,SRR28125661,SRX23770348,SRS20595834,SRP492124,PRJNA1081449,Thymic mimetic cells in zebrafish,GSE259418,Transcriptome Analysis,We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells  a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically  we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067  GSM5732070  GSM5732077   GSM5732078  GSM5732079  GSM5732080  GSM5732081  GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition  we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation  filtering  and cell sorting on a BD FACSAriaII  whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching  filtering  and cell sorting. The live  non autofluorescent  GFP negative  mCherry negative cells a population depleted of T and B cells  thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult  Thymus  3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult  Thymus  4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult  Thymus  1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult  Thymus  2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile  Thymus  1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile  Thymus  2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile  Thymus  3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile  Thymus  4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5,,,,adult thy liberase 1,GSM8115867,,tissue:13 wpf wpf loc name:missing|collection date:missing,adult thy liberase 1,The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms,13 wpf,,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.,tissue:13 wpf,GSM8115867,GSM8115867: adult thy liberase 1; Danio rerio; RNA Seq,GSM8115867 r1,GSM8115867,1,Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics  Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles  i7 index: 8 cycles  i5 index: 0 cycles  Read 2: 91 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP492124,,loader:fastq load.py,adult_thy_liberase_1_S6_L001_I1_001.fastq.gz adult_thy_liberase_1_S6_L001_R1_001.fastq.gz adult_thy_liberase_1_S6_L001_R2_001.fastq.gz,fastq fastq fastq,62862684917.0,494981771.0,GSM8115867 r1,0:8 1:28 2:91,A:12631971877;C:10077821577;G:10579831603;T:11753169367;N:546737,8,28,91,,12631971877,10077821577,10579831603,11753169367,546737,SRX23770348,SRS20595834,,,"Oncology/Hematology, Boston Children's Hospital",1,0.89921,,0.13602,,0.814,,0.55224,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-27,Multi-stage,Multi-stage,Undetermined,Undetermined
33007,SRR29551178,SRX25058395,SRS21755348,SRP516116,PRJNA1128236,The axillary lymphoid organ   an external  experimentally accessible immune organ in the zebrafish,GSE270797,Other,Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals  but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals.  Here  we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin  the pectoral axillary lobe PAL  with a variety of features that make it ideally suited for studying immune cell dynamics in vivo.   This small  transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh like network of fibroblastic reticular cells along which immune cells migrate  and a network of lymphatic vessels draining to a large adjacent lymph sac.  Noninvasive high resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals  and the PAL is readily accessible to external treatment with antigens or pathogens.  This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues  including blood and lymphatic vessels. Overall design: Single cell expression profiling by high throughput sequencing,,pubmed:39091802,,Pectoral axillary lobe scRNA,GSM8352182,,source name:Pectoral axillary lobe|tissue:Pectoral axillary lobe|geo loc name:missing|collection date:missing,Pectoral axillary lobe scRNA,cellranger count v7.0.0 Assembly: zv11 Supplementary files format and content: TSV value and matrix files,Pectoral axillary lobe,,Cell suspension prepared from 4 pectoral axillary lobes 2 from males  2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pectoral axillary lobe,GSM8352182,GSM8352182: Pectoral axillary lobe scRNA; Danio rerio; RNA Seq,GSM8352182 r1,GSM8352182,1,Cell suspension prepared from 4 pectoral axillary lobes 2 from males  2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP516116,,,LCK1_S3_L001_R1_001.fastq.gz LCK1_S3_L001_R2_001.fastq.gz LCK1_S3_L002_R1_001.fastq.gz LCK1_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,21583802440.0,182913580.0,GSM8352182 r1,0:28 1:90,A:6079984051;C:4913875575;G:5182513698;T:5406578531;N:850585,28,90,,,6079984051,4913875575,5182513698,5406578531,850585,SRX25058395,SRS21755348,SRA1909244,"BG 10 RM 8S261, NICHD, NIH","BG 10 RM 8S261, NICHD, NIH",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-06-25,Adult,Adult,Undetermined,Undetermined
33864,SRR30779425,SRX26181412,SRS22725400,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR126,TDR126 10hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:Bud stage 10 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR126 10hpf RNA,TDR126 10hpf RNA EKW NA none 10xmultiome,TDR126 10hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR126 10hpf RNA EKW NA none 10xmultiome S4 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181412,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Gastrula,Embryo,Undetermined,Embryo Imprecise
33865,SRR30779427,SRX26181410,SRS22725399,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR125,TDR125 19hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:20 somites 19 hpf|collection date:2023 09 13|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR125 19hpf RNA,TDR125 19hpf RNA EKW NA none 10xmultiome,TDR125 19hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR125 19hpf RNA EKW NA none 10xmultiome S3 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181410,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Segmentation,Embryo,Undetermined,Embryo Imprecise
33866,SRR30779429,SRX26181408,SRS22725395,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR124,TDR124 24hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:30 somites 24 hpf|collection date:2023 08 17|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR124 24hpf RNA,TDR124 24hpf RNA EKW NA none 10xmultiome,TDR124 24hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR124 24hpf RNA EKW NA none 10xmultiome S2 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181408,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Multi-stage,Embryo,Undetermined,Embryo Imprecise
33867,SRR30779430,SRX26181407,SRS22725398,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR119,TDR119 16hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:15 somites 16 hpf|collection date:2023 06 30|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR119 16hpf RNA,TDR119 16hpf RNA EKW NA none 10xmultiome,TDR119 16hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,137611060524.0,997181598.0,TDR119 16hpf RNA EKW NA none 10xmultiome S2 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:26107486444;C:20041229894;G:22171622563;T:21408164549;N:17840370,10,10,28,90,26107486444,20041229894,22171622563,21408164549,17840370,SRX26181407,SRS22725398,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-24,Segmentation,Embryo,Undetermined,Embryo Imprecise
33868,SRR30779433,SRX26181405,SRS22725397,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR128,TDR128 14hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:10 somites 14 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR128 14hpf RNA,TDR128 14hpf RNA EKW NA none 10xmultiome,TDR128 14hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR128 14hpf RNA EKW NA none 10xmultiome S6 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181405,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Segmentation,Embryo,Undetermined,Embryo Imprecise
33869,SRR30779435,SRX26181403,SRS22725396,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR127,TDR127 12hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:5 somites  12 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR127 12hpf RNA,TDR127 12hpf RNA EKW NA none 10xmultiome,TDR127 12hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR127 12hpf RNA EKW NA none 10xmultiome S5 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181403,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Segmentation,Embryo,Undetermined,Embryo Imprecise
33870,SRR30779437,SRX26181400,SRS22725394,SRP534298,PRJNA1164307,Time resolved single cell Multiomic zebrafish atlas,PRJNA1164307,Other,During development  dynamic interplay between transcription factors  chromatin  and genes  termed gene regulatory network GRN  shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here  we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity  suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework  we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints  but later commit significantly to either lineages. Together  we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.,,,,TDR118,TDR118 16hpf EKW NA none 10xmultiome,,strain:EKW|dev stage:15 somites 16 hpf|collection date:2023 06 23|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal,,,,,,,,,TDR118 16hpf RNA,TDR118 16hpf RNA EKW NA none 10xmultiome,TDR118 16hpf RNA EKW NA none 10xmultiome,10x multiome nuc seq,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534298,,,TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR118 16hpf RNA EKW NA none 10xmultiome S1 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26181400,,SRA1977819,Chan Zuckerberg Biohub San Francisco|Computational Biology,Chan Zuckerberg Biohub San Francisco,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-09-23,Segmentation,Embryo,Undetermined,Embryo Imprecise
34224,SRR31604147,SRX26968916,SRS23437614,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,CV mCherry negative,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Conventionalized|Fluorescence:mCherry negative  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from CV larvae,7066 P3,7066 P3,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,CV_IEC_3_S3_L001_I1_001.fastq.gz CV_IEC_3_S3_L001_R1_001.fastq.gz CV_IEC_3_S3_L001_R2_001.fastq.gz CV_IEC_3_S3_L002_I1_001.fastq.gz CV_IEC_3_S3_L002_R1_001.fastq.gz CV_IEC_3_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,39983364288.0,317328288.0,CV IEC 3 S3 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:7989957184;C:6492876848;G:7106881008;T:6968481488;N:1349392,8,28,90,,7989957184,6492876848,7106881008,6968481488,1349392,SRX26968916,SRS23437614,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34225,SRR31604148,SRX26968915,SRS23437613,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,GF mCherry negative,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Germ free|Fluorescence:mCherry negative  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry negative  GFP positive sorted cells from GF larvae,7066 P1,7066 P1,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,GF_IEC_1_S1_L001_I1_001.fastq.gz GF_IEC_1_S1_L001_R1_001.fastq.gz GF_IEC_1_S1_L001_R2_001.fastq.gz GF_IEC_1_S1_L002_I1_001.fastq.gz GF_IEC_1_S1_L002_R1_001.fastq.gz GF_IEC_1_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,40178994030.0,318880905.0,GF IEC 1 S1 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:8197955224;C:6448684398;G:7158064923;T:6893218597;N:1358308,8,28,90,,8197955224,6448684398,7158064923,6893218597,1358308,SRX26968915,SRS23437613,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34226,SRR31604149,SRX26968914,SRS23437612,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,CV mCherry positive,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Conventionalized|Fluorescence:mCherry positive  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from CV larvae,7066 P4,7066 P4,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,CV_LRE_4_S4_L001_I1_001.fastq.gz CV_LRE_4_S4_L001_R1_001.fastq.gz CV_LRE_4_S4_L001_R2_001.fastq.gz CV_LRE_4_S4_L002_I1_001.fastq.gz CV_LRE_4_S4_L002_R1_001.fastq.gz CV_LRE_4_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,19934299602.0,158208727.0,CV LRE 4 S4 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:4398648037;C:3082182233;G:3214972719;T:3542307593;N:674848,8,28,90,,4398648037,3082182233,3214972719,3542307593,674848,SRX26968914,SRS23437612,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34227,SRR31604150,SRX26968913,SRS23437611,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,GF mCherry positive,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Germ free|Fluorescence:mCherry positive  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from GF larvae,7066 P2,7066 P2,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,GF_LRE_2_S2_L001_I1_001.fastq.gz GF_LRE_2_S2_L001_R1_001.fastq.gz GF_LRE_2_S2_L001_R2_001.fastq.gz GF_LRE_2_S2_L002_I1_001.fastq.gz GF_LRE_2_S2_L002_R1_001.fastq.gz GF_LRE_2_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,16477189470.0,130771345.0,GF LRE 2 S2 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:3664699916;C:2552676887;G:2506770636;T:3044709641;N:563970,8,28,90,,3664699916,2552676887,2506770636,3044709641,563970,SRX26968913,SRS23437611,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
69681,SRR19135481,SRX15203073,SRS12941937,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 7 days,GSM6122392,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 7 days,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122392,GSM6122392: sci 7 days; Danio rerio; RNA Seq,GSM6122392 r1,GSM6122392,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_7d_S1_L001_R1_001.fastq.gz 200326B_SCI_7d_S1_L001_R2_001.fastq.gz,fastq fastq,29475258300.0,98250861.0,GSM6122392 r1,0:150 1:150,A:11751410672;C:5165600847;G:5006614388;T:7550835321;N:797072,150,150,,,11751410672,5165600847,5006614388,7550835321,797072,SRX15203073,SRS12941937,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.84223,0.0,0.39353,1.0,0.74525,,0.54601,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69682,SRR19135482,SRX15203073,SRS12941937,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 7 days,GSM6122392,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 7 days,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122392,GSM6122392: sci 7 days; Danio rerio; RNA Seq,GSM6122392 r1,GSM6122392,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_7d_S1_L002_R1_001.fastq.gz 200326B_SCI_7d_S1_L002_R2_001.fastq.gz,fastq fastq,36747988500.0,122493295.0,GSM6122392 r2,0:150 1:150,A:14654774798;C:6464113495;G:6260198771;T:9367916916;N:984520,150,150,,,14654774798,6464113495,6260198771,9367916916,984520,SRX15203073,SRS12941937,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.84266,0.0,0.38972,1.0,0.74123,,0.55802,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69683,SRR19135483,SRX15203073,SRS12941937,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 7 days,GSM6122392,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 7 days,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122392,GSM6122392: sci 7 days; Danio rerio; RNA Seq,GSM6122392 r1,GSM6122392,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_7d_S1_L003_R1_001.fastq.gz 200326B_SCI_7d_S1_L003_R2_001.fastq.gz,fastq fastq,29317600800.0,97725336.0,GSM6122392 r3,0:150 1:150,A:11710887306;C:5127280140;G:4964728517;T:7513923126;N:781711,150,150,,,11710887306,5127280140,4964728517,7513923126,781711,SRX15203073,SRS12941937,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.84265,0.0,0.3924,1.0,0.74065,,0.5513,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69684,SRR19135484,SRX15203073,SRS12941937,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 7 days,GSM6122392,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 7 days,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122392,GSM6122392: sci 7 days; Danio rerio; RNA Seq,GSM6122392 r1,GSM6122392,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_7d_S1_L004_R1_001.fastq.gz 200326B_SCI_7d_S1_L004_R2_001.fastq.gz,fastq fastq,31023693300.0,103412311.0,GSM6122392 r4,0:150 1:150,A:12411824191;C:5462794848;G:5265823465;T:7882413369;N:837427,150,150,,,12411824191,5462794848,5265823465,7882413369,837427,SRX15203073,SRS12941937,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.84212,0.0,0.38947,1.0,0.74194,,0.55424,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69685,SRR19135485,SRX15203072,SRS12941936,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 1 day,GSM6122391,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 1 day,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122391,GSM6122391: sci 1 day; Danio rerio; RNA Seq,GSM6122391 r1,GSM6122391,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_1d_S1_L001_R1_001.fastq.gz 200326B_SCI_1d_S1_L001_R2_001.fastq.gz,fastq fastq,30796719300.0,102655731.0,GSM6122391 r1,0:150 1:150,A:12350014570;C:5356650438;G:5213090421;T:7876134369;N:829502,150,150,,,12350014570,5356650438,5213090421,7876134369,829502,SRX15203072,SRS12941936,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82474,0.0,0.41531,1.0,0.75676,,0.57108,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69686,SRR19135486,SRX15203072,SRS12941936,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 1 day,GSM6122391,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 1 day,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122391,GSM6122391: sci 1 day; Danio rerio; RNA Seq,GSM6122391 r1,GSM6122391,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_1d_S1_L002_R1_001.fastq.gz 200326B_SCI_1d_S1_L002_R2_001.fastq.gz,fastq fastq,50002460700.0,166674869.0,GSM6122391 r2,0:150 1:150,A:20017686965;C:8776481027;G:8531485975;T:12675453459;N:1353274,150,150,,,20017686965,8776481027,8531485975,12675453459,1353274,SRX15203072,SRS12941936,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82772,0.0,0.41128,1.0,0.75526,,0.57912,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69687,SRR19135487,SRX15203072,SRS12941936,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 1 day,GSM6122391,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 1 day,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122391,GSM6122391: sci 1 day; Danio rerio; RNA Seq,GSM6122391 r1,GSM6122391,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_1d_S1_L003_R1_001.fastq.gz 200326B_SCI_1d_S1_L003_R2_001.fastq.gz,fastq fastq,27393087000.0,91310290.0,GSM6122391 r3,0:150 1:150,A:10993720058;C:4767631453;G:4636926918;T:6994070447;N:738124,150,150,,,10993720058,4767631453,4636926918,6994070447,738124,SRX15203072,SRS12941936,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82551,0.0,0.41348,1.0,0.75463,,0.57216,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69688,SRR19135488,SRX15203072,SRS12941936,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,sci 1 day,GSM6122391,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,sci 1 day,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122391,GSM6122391: sci 1 day; Danio rerio; RNA Seq,GSM6122391 r1,GSM6122391,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_SCI_1d_S1_L004_R1_001.fastq.gz 200326B_SCI_1d_S1_L004_R2_001.fastq.gz,fastq fastq,32242489800.0,107474966.0,GSM6122391 r4,0:150 1:150,A:12933266375;C:5621077845;G:5468451507;T:8218829416;N:864657,150,150,,,12933266375,5621077845,5468451507,8218829416,864657,SRX15203072,SRS12941936,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82532,0.0,0.41398,1.0,0.75605,,0.5687,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69689,SRR19135489,SRX15203071,SRS12941935,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,con,GSM6122390,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,con,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122390,GSM6122390: con; Danio rerio; RNA Seq,GSM6122390 r1,GSM6122390,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_ctrl_S1_L001_R1_001.fastq.gz 200326B_ctrl_S1_L001_R2_001.fastq.gz,fastq fastq,29790064800.0,99300216.0,GSM6122390 r1,0:150 1:150,A:11345104518;C:5411837799;G:5387688262;T:7645052714;N:381507,150,150,,,11345104518,5411837799,5387688262,7645052714,381507,SRX15203071,SRS12941935,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82469,0.0,0.40028,1.0,0.77364,,0.56772,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69690,SRR19135490,SRX15203071,SRS12941935,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,con,GSM6122390,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,con,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122390,GSM6122390: con; Danio rerio; RNA Seq,GSM6122390 r1,GSM6122390,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_ctrl_S1_L002_R1_001.fastq.gz 200326B_ctrl_S1_L002_R2_001.fastq.gz,fastq fastq,35497283400.0,118324278.0,GSM6122390 r2,0:150 1:150,A:13499810877;C:6480615844;G:6449186944;T:9067209386;N:460349,150,150,,,13499810877,6480615844,6449186944,9067209386,460349,SRX15203071,SRS12941935,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82641,0.0,0.39782,1.0,0.7725,,0.57807,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69691,SRR19135491,SRX15203071,SRS12941935,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,con,GSM6122390,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,con,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122390,GSM6122390: con; Danio rerio; RNA Seq,GSM6122390 r1,GSM6122390,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_ctrl_S1_L003_R1_001.fastq.gz 200326B_ctrl_S1_L003_R2_001.fastq.gz,fastq fastq,35833932300.0,119446441.0,GSM6122390 r3,0:150 1:150,A:13602986352;C:6579327464;G:6541522676;T:9109635350;N:460458,150,150,,,13602986352,6579327464,6541522676,9109635350,460458,SRX15203071,SRS12941935,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82721,0.0,0.3953,1.0,0.77165,,0.57432,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
69692,SRR19135492,SRX15203071,SRS12941935,SRP374105,PRJNA836108,Single cell sequencing data of zebrafish spinal cord injury,GSE202429,Transcriptome Analysis,post spinal cord injury in adult zebrafish  the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing,,,,con,GSM6122390,,tissue:Wild type zebrafish|age:4 month|geo loc name:missing|collection date:missing,con,The Cell Ranger software was obtained from 10x Genomics website   https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment  filtering    barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode   matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle   compoments were used to generate clusters by K means algorithm and graph based algorithm  respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count  for every gene and every sample,Wild type zebrafish,,single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction  Single cell RNA seq libraries were   constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,age:4 month,GSM6122390,GSM6122390: con; Danio rerio; RNA Seq,GSM6122390 r1,GSM6122390,1,single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction  Single cell RNA seq libraries were   constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina   Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading   strategy,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP374105,,,200326B_ctrl_S1_L004_R1_001.fastq.gz 200326B_ctrl_S1_L004_R2_001.fastq.gz,fastq fastq,29912840700.0,99709469.0,GSM6122390 r4,0:150 1:150,A:11383688634;C:5482496317;G:5445959161;T:7600315635;N:380953,150,150,,,11383688634,5482496317,5445959161,7600315635,380953,SRX15203071,SRS12941935,SRA1416672,"?????????, ????, ????","神经再生重点实验室, 神经再生, 南通大学",2,0.0,0.82874,0.0,0.39718,1.0,0.77386,,0.58106,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-05-07,Adult,Adult,Undetermined,Undetermined
72589,SRR22838795,SRX18797976,SRS16231609,SRP414185,PRJNA914428,Single cell RNA sequencing scRNA seq of GFP+cells isolated from TgBrn3c:mGFP 6 days zebrafish with GFP expression in all hair cells.,GSE221471,Other,Hair cells play key roles in hearing and balance  and hair cell loss would result in hearing loss or vestibular dysfunction. Zebrafsh  owing to their hair cell enriched organs  have been widely applied in hair cell related research worldwide. In this study  we analyzed the GFP+cells isolated from TgBrn3c:mGFP larvae with GFP expression in all hair cells using single cell RNA sequencing scRNA seq. Three subtypes of hair cells  namely macula hair cell MHC  crista hair cell CHC  and neuromast hair cell NHC  were characterized and validated by whole mount in situ hybridization analysis of marker genes. The hair cell scRNA seq data revealed hair cell specifc genes  including hearing loss genes that have been identifed in humans and novel genes potentially involved in hair cell formation and function. Overall design: Zebrafsh were maintained at 28.5 °C. The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform,,pubmed:35753015,,GFP+  scRNAseq,GSM6873779,,tissue:GFP+cells from TgBrn3c:mGFP zebrafish|cell type:hair cell|age:6 days,GFP+  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: FASTQ,GFP+cells from TgBrn3c:mGFP zebrafish,,The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,cell type:hair cell|age:6 days,GSM6873779,GSM6873779: GFP+  scRNAseq; Danio rerio; RNA Seq,GSM6873779 r1,GSM6873779,1,The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10×Genomics platform. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP414185,,,brn3c6dpf_R1.fq.gz brn3c6dpf_R2.fq.gz,fastq fastq,201407352000.0,671357840.0,GSM6873779 r1,0:150 1:150,A:47653455771;C:37496314066;G:61110504409;T:55144480424;N:2597330,150,150,,,47653455771,37496314066,61110504409,55144480424,2597330,SRX18797976,SRS16231609,SRA1563296,Nantong University,Nantong University,2,0.0,0.90004,0.0,0.18176,1.0,0.76794,,0.55523,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-12-20,Larval,Larval,Undetermined,Undetermined