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
52171,SRR10902876,SRX7571046,SRS6006647,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,24hpf 2,GSM4274622,,source name:embryo|strain:Tubingen|tissue:embryo|genotype:wild type,24hpf 2,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,embryo,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:embryo|genotype:wild type,GSM4274622,GSM4274622: 24hpf 2; Danio rerio; RNA Seq,GSM4274622,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274622,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,24hpf2.bam,bam,30695841720.0,101641860.0,GSM4274622 r1,0:151 1:151,A:8070725571;C:5211775632;G:5264888732;T:12140996276;N:7455509,151,151,,,8070725571,5211775632,5264888732,12140996276,7455509,SRX7571046,SRS6006647,SRA880843,GEO,Zhejiang University,2,2e-05,0.70368,0.0,0.01983,0.99997,0.84774,1.0,0.49229,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
52172,SRR10902875,SRX7571045,SRS6006646,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,24hpf 1,GSM4274621,,source name:embryo|strain:Tubingen|tissue:embryo|genotype:wild type,24hpf 1,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,embryo,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:embryo|genotype:wild type,GSM4274621,GSM4274621: 24hpf 1; Danio rerio; RNA Seq,GSM4274621,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274621,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,24hpf1.bam,bam,36227583572.0,119958886.0,GSM4274621 r1,0:151 1:151,A:9526054168;C:6077203407;G:6186063574;T:14428929871;N:9332552,151,151,,,9526054168,6077203407,6186063574,14428929871,9332552,SRX7571045,SRS6006646,SRA880843,GEO,Zhejiang University,2,0.0,0.68951,0.0,0.01901,1.0,0.85173,,0.47896,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
64506,SRR17299063,SRX13476323,SRS11373166,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL58,GSM5746868,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL58,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746868,GSM5746868: Microwell seq datasets of Zebrafish 24hpf COL58; Danio rerio; RNA Seq,GSM5746868,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL58.bam,bam,91823975304.0,527723996.0,GSM5746868 r1,0:24 1:150,A:27162173122;C:19911517883;G:21018214314;T:23663599459;N:68470526,24,150,,,27162173122,19911517883,21018214314,23663599459,68470526,SRX13476323,SRS11373166,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00273,0.74807,0.00242,0.067,0.99949,0.84889,0.32,0.62031,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64507,SRR17299062,SRX13476322,SRS11373165,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL57,GSM5746867,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL57,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746867,GSM5746867: Microwell seq datasets of Zebrafish 24hpf COL57; Danio rerio; RNA Seq,GSM5746867,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL57.bam,bam,83668974276.0,480856174.0,GSM5746867 r1,0:24 1:150,A:24589284117;C:18203396283;G:19071978317;T:21739883658;N:64431901,24,150,,,24589284117,18203396283,19071978317,21739883658,64431901,SRX13476322,SRS11373165,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00288,0.75168,0.00269,0.07335,0.99969,0.84419,0.6,0.6312,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64508,SRR17299061,SRX13476321,SRS11373164,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL56,GSM5746866,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL56,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746866,GSM5746866: Microwell seq datasets of Zebrafish 24hpf COL56; Danio rerio; RNA Seq,GSM5746866,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL56.bam,bam,86257073418.0,495730307.0,GSM5746866 r1,0:24 1:150,A:25447223471;C:18668491192;G:19647110520;T:22426583347;N:67664888,24,150,,,25447223471,18668491192,19647110520,22426583347,67664888,SRX13476321,SRS11373164,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00275,0.73434,0.00255,0.07548,0.99967,0.84325,0.4375,0.5398,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64509,SRR17299060,SRX13476320,SRS11373163,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL55,GSM5746865,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL55,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746865,GSM5746865: Microwell seq datasets of Zebrafish 24hpf COL55; Danio rerio; RNA Seq,GSM5746865,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL55.bam,bam,90331122120.0,519144380.0,GSM5746865 r1,0:24 1:150,A:26895594483;C:19418243460;G:20453276913;T:23498626121;N:65381143,24,150,,,26895594483,19418243460,20453276913,23498626121,65381143,SRX13476320,SRS11373163,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00295,0.73613,0.00277,0.07262,0.99971,0.83926,0.66666,0.56101,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64510,SRR17299059,SRX13476319,SRS11373162,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL53,GSM5746864,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL53,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746864,GSM5746864: Microwell seq datasets of Zebrafish 24hpf COL53; Danio rerio; RNA Seq,GSM5746864,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL53.bam,bam,89040837126.0,511728949.0,GSM5746864 r1,0:24 1:150,A:26403646377;C:19129690981;G:20273444200;T:23171059435;N:62996133,24,150,,,26403646377,19129690981,20273444200,23171059435,62996133,SRX13476319,SRS11373162,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00256,0.73401,0.00242,0.07541,0.99977,0.83731,0.36363,0.56119,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64511,SRR17299058,SRX13476318,SRS11373161,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL52,GSM5746863,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL52,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746863,GSM5746863: Microwell seq datasets of Zebrafish 24hpf COL52; Danio rerio; RNA Seq,GSM5746863,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL52.bam,bam,92071528062.0,529146713.0,GSM5746863 r1,0:24 1:150,A:27250499787;C:19863195558;G:21006813218;T:23884436340;N:66583159,24,150,,,27250499787,19863195558,21006813218,23884436340,66583159,SRX13476318,SRS11373161,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00303,0.73044,0.00285,0.07319,0.99969,0.84118,0.6,0.55998,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64512,SRR17299057,SRX13476317,SRS11373160,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL51,GSM5746862,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL51,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746862,GSM5746862: Microwell seq datasets of Zebrafish 24hpf COL51; Danio rerio; RNA Seq,GSM5746862,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL51.bam,bam,89393336592.0,513754808.0,GSM5746862 r1,0:24 1:150,A:26357157407;C:19229237017;G:20353675917;T:23391840285;N:61425966,24,150,,,26357157407,19229237017,20353675917,23391840285,61425966,SRX13476317,SRS11373160,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00318,0.74297,0.003,0.07874,0.99969,0.83481,0.6,0.58428,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64513,SRR17299056,SRX13476316,SRS11373159,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 24hpf COL50,GSM5746861,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL50,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746861,GSM5746861: Microwell seq datasets of Zebrafish 24hpf COL50; Danio rerio; RNA Seq,GSM5746861,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL50.bam,bam,93180912216.0,535522484.0,GSM5746861 r1,0:24 1:150,A:27511179288;C:19943495783;G:21163186103;T:24482014463;N:81036579,24,150,,,27511179288,19943495783,21163186103,24482014463,81036579,SRX13476316,SRS11373159,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00287,0.73081,0.00269,0.08165,0.99969,0.83469,0.53333,0.56313,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64962,SRR15293962,SRX11598734,SRS9635704,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Micorwell seq datasets of Zebrafish 24h COL2,GSM5484286,,source name:Zebrafish 24h COL|strain:AB|age:24 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 24h COL2,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24h COL,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5484286,GSM5484286: Micorwell seq datasets of Zebrafish 24h COL2; Danio rerio; RNA Seq,GSM5484286,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5484286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24h_COL2.bam,bam,30695841720.0,101641860.0,GSM5484286 r1,0:151 1:151,A:8070725571;C:5211775632;G:5264888732;T:12140996276;N:7455509,151,151,,,8070725571,5211775632,5264888732,12140996276,7455509,SRX11598734,SRS9635704,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,2e-05,0.70367,0.0,0.01973,0.99997,0.84756,1.0,0.49242,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
64963,SRR15293961,SRX11598733,SRS9635703,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Micorwell seq datasets of Zebrafish 24h COL1,GSM5484285,,source name:Zebrafish 24h COL|strain:AB|age:24 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 24h COL1,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.,Zebrafish 24h COL,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5484285,GSM5484285: Micorwell seq datasets of Zebrafish 24h COL1; Danio rerio; RNA Seq,GSM5484285,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5484285,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_24h_COL1.bam,bam,36227583572.0,119958886.0,GSM5484285 r1,0:151 1:151,A:9526054168;C:6077203407;G:6186063574;T:14428929871;N:9332552,151,151,,,9526054168,6077203407,6186063574,14428929871,9332552,SRX11598733,SRS9635703,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.0,0.68952,0.0,0.01903,1.0,0.85167,,0.4788,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures