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 69051,SRR18432286,SRX14566130,SRS12343128,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL16,GSM5965364,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL16,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965364,GSM5965364: Micorwell seq datasets of Zebrafish 22m COL16; Danio rerio; RNA Seq,GSM5965364 r1,GSM5965364,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL16_1_2.fq.gz Zebrafish_22m_COL16_1_1.fq.gz,fastq fastq,5552134200.0,37014228.0,GSM5965364 r1,0:150 1:150,A:1636845386;C:1022282341;G:1050955671;T:1840072791;N:1978011,150,150,,,1636845386,1022282341,1050955671,1840072791,1978011,SRX14566130,SRS12343128,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35479,,0.01916,,0.9027,,0.32422,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69052,SRR19368199,SRX14566130,SRS12343128,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL16,GSM5965364,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL16,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965364,GSM5965364: Micorwell seq datasets of Zebrafish 22m COL16; Danio rerio; RNA Seq,GSM5965364 r1,GSM5965364,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL16_2_2.fq.gz Zebrafish_22m_COL16_2_1.fq.gz,fastq fastq,20024400906.0,155227914.0,GSM5965364 r2,0:108 1:150,A:5865242054;C:4019481498;G:4311025389;T:5800102838;N:28549127,108,150,,,5865242054,4019481498,4311025389,5800102838,28549127,SRX14566130,SRS12343128,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40431,,0.02236,,0.93072,,0.32634,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69053,SRR19600339,SRX14566130,SRS12343128,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL16,GSM5965364,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL16,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965364,GSM5965364: Micorwell seq datasets of Zebrafish 22m COL16; Danio rerio; RNA Seq,GSM5965364 r1,GSM5965364,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL16_3_1.fq.gz Zebrafish_22m_COL16_3_2.fq.gz,fastq fastq,12494363190.0,143613370.0,GSM5965364 r3,0:24 1:150,A:4260245103;C:2479681600;G:2487270882;T:3219352443;N:47813162,24,150,,,4260245103,2479681600,2487270882,3219352443,47813162,SRX14566130,SRS12343128,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35862,,0.01881,,0.92533,,0.31978,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69054,SRR20230002,SRX14566130,SRS12343128,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL16,GSM5965364,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL16,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965364,GSM5965364: Micorwell seq datasets of Zebrafish 22m COL16; Danio rerio; RNA Seq,GSM5965364 r1,GSM5965364,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL16_4_2.fq.gz Zebrafish_22m_COL16_4_1.fq.gz,fastq fastq,12056306010.0,138578230.0,GSM5965364 r4,0:24 1:150,A:4104157347;C:2392920312;G:2417101695;T:3111018454;N:31108202,24,150,,,4104157347,2392920312,2417101695,3111018454,31108202,SRX14566130,SRS12343128,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37092,,0.01949,,0.92285,,0.32523,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69055,SRR18432287,SRX14566129,SRS12343126,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL15,GSM5965363,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL15,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965363,GSM5965363: Micorwell seq datasets of Zebrafish 22m COL15; Danio rerio; RNA Seq,GSM5965363 r1,GSM5965363,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL15_1_1.fq.gz Zebrafish_22m_COL15_1_2.fq.gz,fastq fastq,6123756000.0,40825040.0,GSM5965363 r1,0:150 1:150,A:1827542171;C:1117092612;G:1145436206;T:2031519720;N:2165291,150,150,,,1827542171,1117092612,1145436206,2031519720,2165291,SRX14566129,SRS12343126,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.33851,,0.01733,,0.90851,,0.34471,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69056,SRR19368198,SRX14566129,SRS12343126,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL15,GSM5965363,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL15,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965363,GSM5965363: Micorwell seq datasets of Zebrafish 22m COL15; Danio rerio; RNA Seq,GSM5965363 r1,GSM5965363,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL15_2_1.fq.gz Zebrafish_22m_COL15_2_2.fq.gz,fastq fastq,20251659174.0,156989606.0,GSM5965363 r2,0:108 1:150,A:5997018976;C:4030988839;G:4300184941;T:5894614720;N:28851698,108,150,,,5997018976,4030988839,4300184941,5894614720,28851698,SRX14566129,SRS12343126,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39137,,0.01731,,0.93253,,0.34073,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69057,SRR19600338,SRX14566129,SRS12343126,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL15,GSM5965363,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL15,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965363,GSM5965363: Micorwell seq datasets of Zebrafish 22m COL15; Danio rerio; RNA Seq,GSM5965363 r1,GSM5965363,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL15_3_1.fq.gz Zebrafish_22m_COL15_3_2.fq.gz,fastq fastq,12521282034.0,143922782.0,GSM5965363 r3,0:24 1:150,A:4315943851;C:2453889901;G:2466547552;T:3236857435;N:48043295,24,150,,,4315943851,2453889901,2466547552,3236857435,48043295,SRX14566129,SRS12343126,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35102,,0.01618,,0.92634,,0.34104,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69058,SRR20230001,SRX14566129,SRS12343126,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL15,GSM5965363,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL15,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965363,GSM5965363: Micorwell seq datasets of Zebrafish 22m COL15; Danio rerio; RNA Seq,GSM5965363 r1,GSM5965363,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL15_4_1.fq.gz Zebrafish_22m_COL15_4_2.fq.gz,fastq fastq,13802844582.0,158653386.0,GSM5965363 r4,0:24 1:150,A:4749278962;C:2705282723;G:2737988540;T:3575482368;N:34811989,24,150,,,4749278962,2705282723,2737988540,3575482368,34811989,SRX14566129,SRS12343126,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36135,,0.0166,,0.92393,,0.33552,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69059,SRR18432288,SRX14566128,SRS12343127,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL14,GSM5965362,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL14,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965362,GSM5965362: Micorwell seq datasets of Zebrafish 22m COL14; Danio rerio; RNA Seq,GSM5965362 r1,GSM5965362,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL14_1_1.fq.gz Zebrafish_22m_COL14_1_2.fq.gz,fastq fastq,7937867700.0,52919118.0,GSM5965362 r1,0:150 1:150,A:2347679790;C:1451399869;G:1493066908;T:2642888183;N:2832950,150,150,,,2347679790,1451399869,1493066908,2642888183,2832950,SRX14566128,SRS12343127,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35121,,0.01702,,0.90498,,0.34557,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69060,SRR19368197,SRX14566128,SRS12343127,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL14,GSM5965362,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL14,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965362,GSM5965362: Micorwell seq datasets of Zebrafish 22m COL14; Danio rerio; RNA Seq,GSM5965362 r1,GSM5965362,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL14_2_1.fq.gz Zebrafish_22m_COL14_2_2.fq.gz,fastq fastq,25651177086.0,198846334.0,GSM5965362 r2,0:108 1:150,A:7546130806;C:5110163809;G:5472375471;T:7485985875;N:36521125,108,150,,,7546130806,5110163809,5472375471,7485985875,36521125,SRX14566128,SRS12343127,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3996,,0.01837,,0.92999,,0.34348,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69061,SRR19600337,SRX14566128,SRS12343127,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL14,GSM5965362,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL14,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965362,GSM5965362: Micorwell seq datasets of Zebrafish 22m COL14; Danio rerio; RNA Seq,GSM5965362 r1,GSM5965362,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL14_3_1.fq.gz Zebrafish_22m_COL14_3_2.fq.gz,fastq fastq,15639947370.0,179769510.0,GSM5965362 r3,0:24 1:150,A:5301780511;C:3089311667;G:3114099586;T:4075104801;N:59650805,24,150,,,5301780511,3089311667,3114099586,4075104801,59650805,SRX14566128,SRS12343127,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36342,,0.01616,,0.92328,,0.34207,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69062,SRR20230000,SRX14566128,SRS12343127,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL14,GSM5965362,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL14,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965362,GSM5965362: Micorwell seq datasets of Zebrafish 22m COL14; Danio rerio; RNA Seq,GSM5965362 r1,GSM5965362,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL14_4_1.fq.gz Zebrafish_22m_COL14_4_2.fq.gz,fastq fastq,17288243454.0,198715442.0,GSM5965362 r4,0:24 1:150,A:5860531507;C:3414928706;G:3460319121;T:4511234423;N:41229697,24,150,,,5860531507,3414928706,3460319121,4511234423,41229697,SRX14566128,SRS12343127,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36857,,0.01762,,0.92411,,0.33601,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69063,SRR18432289,SRX14566127,SRS12343125,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL13,GSM5965361,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL13,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965361,GSM5965361: Micorwell seq datasets of Zebrafish 22m COL13; Danio rerio; RNA Seq,GSM5965361 r1,GSM5965361,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL13_1_1.fq.gz Zebrafish_22m_COL13_1_2.fq.gz,fastq fastq,6723967500.0,44826450.0,GSM5965361 r1,0:150 1:150,A:1980244686;C:1231063602;G:1268605159;T:2241701674;N:2352379,150,150,,,1980244686,1231063602,1268605159,2241701674,2352379,SRX14566127,SRS12343125,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34641,,0.01727,,0.90122,,0.35974,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69064,SRR19368196,SRX14566127,SRS12343125,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL13,GSM5965361,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL13,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965361,GSM5965361: Micorwell seq datasets of Zebrafish 22m COL13; Danio rerio; RNA Seq,GSM5965361 r1,GSM5965361,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL13_2_1.fq.gz Zebrafish_22m_COL13_2_2.fq.gz,fastq fastq,21719541660.0,168368540.0,GSM5965361 r2,0:108 1:150,A:6351154824;C:4341538719;G:4653736802;T:6341921932;N:31189383,108,150,,,6351154824,4341538719,4653736802,6341921932,31189383,SRX14566127,SRS12343125,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38949,,0.01781,,0.92817,,0.35286,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69065,SRR19600336,SRX14566127,SRS12343125,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL13,GSM5965361,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL13,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965361,GSM5965361: Micorwell seq datasets of Zebrafish 22m COL13; Danio rerio; RNA Seq,GSM5965361 r1,GSM5965361,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL13_3_1.fq.gz Zebrafish_22m_COL13_3_2.fq.gz,fastq fastq,13392521088.0,153937024.0,GSM5965361 r3,0:24 1:150,A:4517365726;C:2661512352;G:2691459833;T:3471368645;N:50814532,24,150,,,4517365726,2661512352,2691459833,3471368645,50814532,SRX14566127,SRS12343125,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35965,,0.01616,,0.9194,,0.36288,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69066,SRR20229999,SRX14566127,SRS12343125,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL13,GSM5965361,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL13,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965361,GSM5965361: Micorwell seq datasets of Zebrafish 22m COL13; Danio rerio; RNA Seq,GSM5965361 r1,GSM5965361,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL13_4_1.fq.gz Zebrafish_22m_COL13_4_2.fq.gz,fastq fastq,14625067836.0,168104228.0,GSM5965361 r4,0:24 1:150,A:4925303460;C:2903042925;G:2956946846;T:3805663780;N:34110825,24,150,,,4925303460,2903042925,2956946846,3805663780,34110825,SRX14566127,SRS12343125,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36845,,0.01714,,0.91857,,0.35645,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69067,SRR18432290,SRX14566126,SRS12343124,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL128,GSM5965379,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL128,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965379,GSM5965379: Micorwell seq datasets of Zebrafish 22m COL128; Danio rerio; RNA Seq,GSM5965379 r1,GSM5965379,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL128_1_1.fq.gz Zebrafish_22m_COL128_1_2.fq.gz,fastq fastq,5789740200.0,38598268.0,GSM5965379 r1,0:150 1:150,A:1701206278;C:1064415425;G:1096082893;T:1925959068;N:2076536,150,150,,,1701206278,1064415425,1096082893,1925959068,2076536,SRX14566126,SRS12343124,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3531,,0.02196,,0.88527,,0.39698,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69068,SRR19574850,SRX14566126,SRS12343124,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL128,GSM5965379,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL128,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965379,GSM5965379: Micorwell seq datasets of Zebrafish 22m COL128; Danio rerio; RNA Seq,GSM5965379 r1,GSM5965379,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL128_2_2.fq.gz Zebrafish_22m_COL128_2_1.fq.gz,fastq fastq,18260584164.0,141554916.0,GSM5965379 r2,0:108 1:150,A:5285028528;C:3719052801;G:3984275987;T:5245280262;N:26946586,108,150,,,5285028528,3719052801,3984275987,5245280262,26946586,SRX14566126,SRS12343124,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.41138,,0.0237,,0.91076,,0.4114,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69069,SRR19600354,SRX14566126,SRS12343124,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL128,GSM5965379,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL128,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965379,GSM5965379: Micorwell seq datasets of Zebrafish 22m COL128; Danio rerio; RNA Seq,GSM5965379 r1,GSM5965379,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL128_3_1.fq.gz Zebrafish_22m_COL128_3_2.fq.gz,fastq fastq,11491275462.0,132083626.0,GSM5965379 r3,0:24 1:150,A:3804995108;C:2313030118;G:2331738932;T:2997442812;N:44068492,24,150,,,3804995108,2313030118,2331738932,2997442812,44068492,SRX14566126,SRS12343124,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37935,,0.021,,0.90187,,0.42088,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69070,SRR20220081,SRX14566126,SRS12343124,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL128,GSM5965379,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL128,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965379,GSM5965379: Micorwell seq datasets of Zebrafish 22m COL128; Danio rerio; RNA Seq,GSM5965379 r1,GSM5965379,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL128_4_2.fq.gz Zebrafish_22m_COL128_4_1.fq.gz,fastq fastq,12069048552.0,138724696.0,GSM5965379 r4,0:24 1:150,A:3979468311;C:2428210527;G:2466041386;T:3165030970;N:30297358,24,150,,,3979468311,2428210527,2466041386,3165030970,30297358,SRX14566126,SRS12343124,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38971,,0.02244,,0.9013,,0.41727,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69071,SRR18432291,SRX14566125,SRS12343123,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL127,GSM5965378,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL127,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965378,GSM5965378: Micorwell seq datasets of Zebrafish 22m COL127; Danio rerio; RNA Seq,GSM5965378 r1,GSM5965378,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL127_1_2.fq.gz Zebrafish_22m_COL127_1_1.fq.gz,fastq fastq,5124860400.0,34165736.0,GSM5965378 r1,0:150 1:150,A:1513961185;C:939406925;G:966814069;T:1702869054;N:1809167,150,150,,,1513961185,939406925,966814069,1702869054,1809167,SRX14566125,SRS12343123,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35356,,0.02035,,0.88976,,0.43439,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69072,SRR19574849,SRX14566125,SRS12343123,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL127,GSM5965378,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL127,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965378,GSM5965378: Micorwell seq datasets of Zebrafish 22m COL127; Danio rerio; RNA Seq,GSM5965378 r1,GSM5965378,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL127_2_2.fq.gz Zebrafish_22m_COL127_2_1.fq.gz,fastq fastq,15861017238.0,122953622.0,GSM5965378 r2,0:108 1:150,A:4643583257;C:3213962529;G:3423607667;T:4557847117;N:22016668,108,150,,,4643583257,3213962529,3423607667,4557847117,22016668,SRX14566125,SRS12343123,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.4086,,0.02002,,0.91311,,0.42538,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69073,SRR19600353,SRX14566125,SRS12343123,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL127,GSM5965378,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL127,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965378,GSM5965378: Micorwell seq datasets of Zebrafish 22m COL127; Danio rerio; RNA Seq,GSM5965378 r1,GSM5965378,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL127_3_2.fq.gz Zebrafish_22m_COL127_3_1.fq.gz,fastq fastq,10111844004.0,116228092.0,GSM5965378 r3,0:24 1:150,A:3426096949;C:2025276920;G:2033325552;T:2588909029;N:38235554,24,150,,,3426096949,2025276920,2033325552,2588909029,38235554,SRX14566125,SRS12343123,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36967,,0.01861,,0.90826,,0.42287,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69074,SRR20220080,SRX14566125,SRS12343123,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL127,GSM5965378,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL127,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965378,GSM5965378: Micorwell seq datasets of Zebrafish 22m COL127; Danio rerio; RNA Seq,GSM5965378 r1,GSM5965378,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL127_4_2.fq.gz Zebrafish_22m_COL127_4_1.fq.gz,fastq fastq,10474478100.0,120396300.0,GSM5965378 r4,0:24 1:150,A:3531885021;C:2101499672;G:2125519634;T:2689761823;N:25811950,24,150,,,3531885021,2101499672,2125519634,2689761823,25811950,SRX14566125,SRS12343123,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3798,,0.01867,,0.90636,,0.42028,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69075,SRR18432292,SRX14566124,SRS12343122,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL126,GSM5965377,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL126,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965377,GSM5965377: Micorwell seq datasets of Zebrafish 22m COL126; Danio rerio; RNA Seq,GSM5965377 r1,GSM5965377,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL126_1_1.fq.gz Zebrafish_22m_COL126_1_2.fq.gz,fastq fastq,7003662300.0,46691082.0,GSM5965377 r1,0:150 1:150,A:2061319597;C:1285353344;G:1326044685;T:2328446534;N:2498140,150,150,,,2061319597,1285353344,1326044685,2328446534,2498140,SRX14566124,SRS12343122,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37323,,0.02115,,0.8788,,0.40349,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69076,SRR19574848,SRX14566124,SRS12343122,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL126,GSM5965377,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL126,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965377,GSM5965377: Micorwell seq datasets of Zebrafish 22m COL126; Danio rerio; RNA Seq,GSM5965377 r1,GSM5965377,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL126_2_1.fq.gz Zebrafish_22m_COL126_2_2.fq.gz,fastq fastq,21928621248.0,169989312.0,GSM5965377 r2,0:108 1:150,A:6346880159;C:4470144046;G:4792025986;T:6287831916;N:31739141,108,150,,,6346880159,4470144046,4792025986,6287831916,31739141,SRX14566124,SRS12343122,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.43432,,0.02183,,0.90575,,0.39174,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69077,SRR19600352,SRX14566124,SRS12343122,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL126,GSM5965377,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL126,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965377,GSM5965377: Micorwell seq datasets of Zebrafish 22m COL126; Danio rerio; RNA Seq,GSM5965377 r1,GSM5965377,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL126_3_1.fq.gz Zebrafish_22m_COL126_3_2.fq.gz,fastq fastq,14450087868.0,166092964.0,GSM5965377 r3,0:24 1:150,A:4824133345;C:2912799030;G:2934060583;T:3724135564;N:54959346,24,150,,,4824133345,2912799030,2934060583,3724135564,54959346,SRX14566124,SRS12343122,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39602,,0.01941,,0.89769,,0.38858,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69078,SRR20220079,SRX14566124,SRS12343122,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL126,GSM5965377,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL126,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965377,GSM5965377: Micorwell seq datasets of Zebrafish 22m COL126; Danio rerio; RNA Seq,GSM5965377 r1,GSM5965377,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL126_4_1.fq.gz Zebrafish_22m_COL126_4_2.fq.gz,fastq fastq,14418347832.0,165728136.0,GSM5965377 r4,0:24 1:150,A:4806960323;C:2902055766;G:2940914581;T:3732482781;N:35934381,24,150,,,4806960323,2902055766,2940914581,3732482781,35934381,SRX14566124,SRS12343122,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40514,,0.02038,,0.89913,,0.39216,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69079,SRR18432293,SRX14566123,SRS12343121,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL125,GSM5965376,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL125,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965376,GSM5965376: Micorwell seq datasets of Zebrafish 22m COL125; Danio rerio; RNA Seq,GSM5965376 r1,GSM5965376,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL125_1_2.fq.gz Zebrafish_22m_COL125_1_1.fq.gz,fastq fastq,7459754700.0,49731698.0,GSM5965376 r1,0:150 1:150,A:2202127456;C:1356920652;G:1395024764;T:2503038567;N:2643261,150,150,,,2202127456,1356920652,1395024764,2503038567,2643261,SRX14566123,SRS12343121,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35096,,0.02065,,0.88473,,0.4206,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69080,SRR19574847,SRX14566123,SRS12343121,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL125,GSM5965376,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL125,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965376,GSM5965376: Micorwell seq datasets of Zebrafish 22m COL125; Danio rerio; RNA Seq,GSM5965376 r1,GSM5965376,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL125_2_2.fq.gz Zebrafish_22m_COL125_2_1.fq.gz,fastq fastq,23224735332.0,180036708.0,GSM5965376 r2,0:108 1:150,A:6825136740;C:4630631087;G:4922314761;T:6813871375;N:32781369,108,150,,,6825136740,4630631087,4922314761,6813871375,32781369,SRX14566123,SRS12343121,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38882,,0.01974,,0.91648,,0.38999,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69081,SRR19600351,SRX14566123,SRS12343121,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL125,GSM5965376,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL125,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965376,GSM5965376: Micorwell seq datasets of Zebrafish 22m COL125; Danio rerio; RNA Seq,GSM5965376 r1,GSM5965376,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL125_3_2.fq.gz Zebrafish_22m_COL125_3_1.fq.gz,fastq fastq,14655034638.0,168448674.0,GSM5965376 r3,0:24 1:150,A:5009311509;C:2883440232;G:2900401494;T:3806267923;N:55613480,24,150,,,5009311509,2883440232,2900401494,3806267923,55613480,SRX14566123,SRS12343121,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35367,,0.01773,,0.90938,,0.41229,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69082,SRR20220078,SRX14566123,SRS12343121,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL125,GSM5965376,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL125,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965376,GSM5965376: Micorwell seq datasets of Zebrafish 22m COL125; Danio rerio; RNA Seq,GSM5965376 r1,GSM5965376,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL125_4_2.fq.gz Zebrafish_22m_COL125_4_1.fq.gz,fastq fastq,16384573932.0,188328436.0,GSM5965376 r4,0:24 1:150,A:5573088586;C:3227582702;G:3281220371;T:4263171568;N:39510705,24,150,,,5573088586,3227582702,3281220371,4263171568,39510705,SRX14566123,SRS12343121,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36265,,0.0186,,0.90713,,0.41077,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69083,SRR18432294,SRX14566122,SRS12343120,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL124,GSM5965375,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL124,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965375,GSM5965375: Micorwell seq datasets of Zebrafish 22m COL124; Danio rerio; RNA Seq,GSM5965375 r1,GSM5965375,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL124_1_2.fq.gz Zebrafish_22m_COL124_1_1.fq.gz,fastq fastq,6105326700.0,40702178.0,GSM5965375 r1,0:150 1:150,A:1803834538;C:1098189676;G:1136327295;T:2064805156;N:2170035,150,150,,,1803834538,1098189676,1136327295,2064805156,2170035,SRX14566122,SRS12343120,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.33864,,0.02468,,0.85947,,0.53239,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69084,SRR19574846,SRX14566122,SRS12343120,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL124,GSM5965375,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL124,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965375,GSM5965375: Micorwell seq datasets of Zebrafish 22m COL124; Danio rerio; RNA Seq,GSM5965375 r1,GSM5965375,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL124_2_1.fq.gz Zebrafish_22m_COL124_2_2.fq.gz,fastq fastq,18767022684.0,145480796.0,GSM5965375 r2,0:108 1:150,A:5499983693;C:3738268199;G:4008262572;T:5493533720;N:26974500,108,150,,,5499983693,3738268199,4008262572,5493533720,26974500,SRX14566122,SRS12343120,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38758,,0.02632,,0.88793,,0.52969,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69085,SRR19600350,SRX14566122,SRS12343120,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL124,GSM5965375,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL124,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965375,GSM5965375: Micorwell seq datasets of Zebrafish 22m COL124; Danio rerio; RNA Seq,GSM5965375 r1,GSM5965375,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL124_3_1.fq.gz Zebrafish_22m_COL124_3_2.fq.gz,fastq fastq,11191217334.0,128634682.0,GSM5965375 r3,0:24 1:150,A:3736622449;C:2233397703;G:2263151822;T:2915186080;N:42859280,24,150,,,3736622449,2233397703,2263151822,2915186080,42859280,SRX14566122,SRS12343120,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36729,,0.02544,,0.8744,,0.52585,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69086,SRR20220077,SRX14566122,SRS12343120,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL124,GSM5965375,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL124,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965375,GSM5965375: Micorwell seq datasets of Zebrafish 22m COL124; Danio rerio; RNA Seq,GSM5965375 r1,GSM5965375,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL124_4_1.fq.gz Zebrafish_22m_COL124_4_2.fq.gz,fastq fastq,12106626636.0,139156628.0,GSM5965375 r4,0:24 1:150,A:4068592712;C:2396243390;G:2451448462;T:3160700967;N:29641105,24,150,,,4068592712,2396243390,2451448462,3160700967,29641105,SRX14566122,SRS12343120,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36914,,0.02593,,0.87426,,0.50849,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69087,SRR18432295,SRX14566121,SRS12343119,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL123,GSM5965374,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL123,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965374,GSM5965374: Micorwell seq datasets of Zebrafish 22m COL123; Danio rerio; RNA Seq,GSM5965374 r1,GSM5965374,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL123_1_2.fq.gz Zebrafish_22m_COL123_1_1.fq.gz,fastq fastq,7147484700.0,47649898.0,GSM5965374 r1,0:150 1:150,A:2105784861;C:1290305310;G:1328822195;T:2419990741;N:2581593,150,150,,,2105784861,1290305310,1328822195,2419990741,2581593,SRX14566121,SRS12343119,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35477,,0.0246,,0.86354,,0.51177,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69088,SRR19574845,SRX14566121,SRS12343119,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL123,GSM5965374,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL123,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965374,GSM5965374: Micorwell seq datasets of Zebrafish 22m COL123; Danio rerio; RNA Seq,GSM5965374 r1,GSM5965374,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL123_2_2.fq.gz Zebrafish_22m_COL123_2_1.fq.gz,fastq fastq,22363798620.0,173362780.0,GSM5965374 r2,0:108 1:150,A:6486427621;C:4486668356;G:4799953515;T:6558055329;N:32693799,108,150,,,6486427621,4486668356,4799953515,6558055329,32693799,SRX14566121,SRS12343119,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40476,,0.0263,,0.89388,,0.53794,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69089,SRR19600349,SRX14566121,SRS12343119,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL123,GSM5965374,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL123,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965374,GSM5965374: Micorwell seq datasets of Zebrafish 22m COL123; Danio rerio; RNA Seq,GSM5965374 r1,GSM5965374,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL123_3_1.fq.gz Zebrafish_22m_COL123_3_2.fq.gz,fastq fastq,13639629450.0,156777350.0,GSM5965374 r3,0:24 1:150,A:4543944737;C:2714426130;G:2729190733;T:3600152053;N:51915797,24,150,,,4543944737,2714426130,2729190733,3600152053,51915797,SRX14566121,SRS12343119,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3793,,0.02427,,0.884,,0.53254,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69090,SRR20220076,SRX14566121,SRS12343119,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL123,GSM5965374,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL123,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965374,GSM5965374: Micorwell seq datasets of Zebrafish 22m COL123; Danio rerio; RNA Seq,GSM5965374 r1,GSM5965374,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL123_4_1.fq.gz Zebrafish_22m_COL123_4_2.fq.gz,fastq fastq,15615026394.0,179483062.0,GSM5965374 r4,0:24 1:150,A:5186246724;C:3099168670;G:3152397235;T:4139692003;N:37521762,24,150,,,5186246724,3099168670,3152397235,4139692003,37521762,SRX14566121,SRS12343119,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38836,,0.02406,,0.88266,,0.50307,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69091,SRR18432296,SRX14566120,SRS12343118,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL122,GSM5965373,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL122,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965373,GSM5965373: Micorwell seq datasets of Zebrafish 22m COL122; Danio rerio; RNA Seq,GSM5965373 r1,GSM5965373,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL122_1_1.fq.gz Zebrafish_22m_COL122_1_2.fq.gz,fastq fastq,5025684000.0,33504560.0,GSM5965373 r1,0:150 1:150,A:1490034518;C:901358610;G:931428752;T:1701043337;N:1818783,150,150,,,1490034518,901358610,931428752,1701043337,1818783,SRX14566120,SRS12343118,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34203,,0.02091,,0.87545,,0.49317,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69092,SRR19574844,SRX14566120,SRS12343118,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL122,GSM5965373,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL122,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965373,GSM5965373: Micorwell seq datasets of Zebrafish 22m COL122; Danio rerio; RNA Seq,GSM5965373 r1,GSM5965373,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL122_2_1.fq.gz Zebrafish_22m_COL122_2_2.fq.gz,fastq fastq,16861560846.0,130709774.0,GSM5965373 r2,0:108 1:150,A:4924721195;C:3349456681;G:3597434151;T:4964936243;N:25012576,108,150,,,4924721195,3349456681,3597434151,4964936243,25012576,SRX14566120,SRS12343118,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39315,,0.02107,,0.90335,,0.52604,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69093,SRR19600348,SRX14566120,SRS12343118,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL122,GSM5965373,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL122,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965373,GSM5965373: Micorwell seq datasets of Zebrafish 22m COL122; Danio rerio; RNA Seq,GSM5965373 r1,GSM5965373,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL122_3_1.fq.gz Zebrafish_22m_COL122_3_2.fq.gz,fastq fastq,10462565538.0,120259374.0,GSM5965373 r3,0:24 1:150,A:3529681455;C:2077077055;G:2083884916;T:2731589449;N:40332663,24,150,,,3529681455,2077077055,2083884916,2731589449,40332663,SRX14566120,SRS12343118,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36935,,0.01892,,0.89353,,0.49567,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69094,SRR20220075,SRX14566120,SRS12343118,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL122,GSM5965373,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL122,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965373,GSM5965373: Micorwell seq datasets of Zebrafish 22m COL122; Danio rerio; RNA Seq,GSM5965373 r1,GSM5965373,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL122_4_1.fq.gz Zebrafish_22m_COL122_4_2.fq.gz,fastq fastq,10147432746.0,116637158.0,GSM5965373 r4,0:24 1:150,A:3420445274;C:2012096019;G:2033251161;T:2655437258;N:26203034,24,150,,,3420445274,2012096019,2033251161,2655437258,26203034,SRX14566120,SRS12343118,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37912,,0.02069,,0.89256,,0.4814,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69095,SRR18432297,SRX14566119,SRS12343117,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL121,GSM5965372,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL121,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965372,GSM5965372: Micorwell seq datasets of Zebrafish 22m COL121; Danio rerio; RNA Seq,GSM5965372 r1,GSM5965372,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL121_1_2.fq.gz Zebrafish_22m_COL121_1_1.fq.gz,fastq fastq,6241509900.0,41610066.0,GSM5965372 r1,0:150 1:150,A:1836883392;C:1125115984;G:1158061131;T:2119242701;N:2206692,150,150,,,1836883392,1125115984,1158061131,2119242701,2206692,SRX14566119,SRS12343117,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34767,,0.02389,,0.86561,,0.51404,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69096,SRR19574843,SRX14566119,SRS12343117,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL121,GSM5965372,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL121,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965372,GSM5965372: Micorwell seq datasets of Zebrafish 22m COL121; Danio rerio; RNA Seq,GSM5965372 r1,GSM5965372,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL121_2_1.fq.gz Zebrafish_22m_COL121_2_2.fq.gz,fastq fastq,20381037402.0,157992538.0,GSM5965372 r2,0:108 1:150,A:5924617665;C:4061076664;G:4343030573;T:6022757961;N:29554539,108,150,,,5924617665,4061076664,4343030573,6022757961,29554539,SRX14566119,SRS12343117,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39292,,0.02429,,0.89779,,0.54052,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69097,SRR19600347,SRX14566119,SRS12343117,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL121,GSM5965372,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL121,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965372,GSM5965372: Micorwell seq datasets of Zebrafish 22m COL121; Danio rerio; RNA Seq,GSM5965372 r1,GSM5965372,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL121_3_1.fq.gz Zebrafish_22m_COL121_3_2.fq.gz,fastq fastq,12962573178.0,148995094.0,GSM5965372 r3,0:24 1:150,A:4392997024;C:2545208711;G:2555738892;T:3419806282;N:48822269,24,150,,,4392997024,2545208711,2555738892,3419806282,48822269,SRX14566119,SRS12343117,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36239,,0.0223,,0.89079,,0.54879,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69098,SRR20220074,SRX14566119,SRS12343117,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL121,GSM5965372,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL121,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965372,GSM5965372: Micorwell seq datasets of Zebrafish 22m COL121; Danio rerio; RNA Seq,GSM5965372 r1,GSM5965372,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL121_4_2.fq.gz Zebrafish_22m_COL121_4_1.fq.gz,fastq fastq,13992529638.0,160833674.0,GSM5965372 r4,0:24 1:150,A:4723750519;C:2745683390;G:2786342949;T:3701370605;N:35382175,24,150,,,4723750519,2745683390,2786342949,3701370605,35382175,SRX14566119,SRS12343117,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37133,,0.02324,,0.8888,,0.52811,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69099,SRR18432298,SRX14566118,SRS12343116,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL100,GSM5965371,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL100,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965371,GSM5965371: Micorwell seq datasets of Zebrafish 22m COL100; Danio rerio; RNA Seq,GSM5965371 r1,GSM5965371,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL100_1_2.fq.gz Zebrafish_22m_COL100_1_1.fq.gz,fastq fastq,5393265000.0,35955100.0,GSM5965371 r1,0:150 1:150,A:1595049513;C:979482166;G:1012478232;T:1804365746;N:1889343,150,150,,,1595049513,979482166,1012478232,1804365746,1889343,SRX14566118,SRS12343116,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35087,,0.01883,,0.88805,,0.41722,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69100,SRR19574842,SRX14566118,SRS12343116,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL100,GSM5965371,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL100,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965371,GSM5965371: Micorwell seq datasets of Zebrafish 22m COL100; Danio rerio; RNA Seq,GSM5965371 r1,GSM5965371,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL100_2_2.fq.gz Zebrafish_22m_COL100_2_1.fq.gz,fastq fastq,17121249198.0,132722862.0,GSM5965371 r2,0:108 1:150,A:5012468241;C:3427280964;G:3676770901;T:4980354879;N:24374213,108,150,,,5012468241,3427280964,3676770901,4980354879,24374213,SRX14566118,SRS12343116,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40282,,0.02005,,0.91311,,0.41316,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69101,SRR19600346,SRX14566118,SRS12343116,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL100,GSM5965371,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL100,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965371,GSM5965371: Micorwell seq datasets of Zebrafish 22m COL100; Danio rerio; RNA Seq,GSM5965371 r1,GSM5965371,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL100_3_1.fq.gz Zebrafish_22m_COL100_3_2.fq.gz,fastq fastq,10689663900.0,122869700.0,GSM5965371 r3,0:24 1:150,A:3601577071;C:2127212143;G:2148914414;T:2771385134;N:40575138,24,150,,,3601577071,2127212143,2148914414,2771385134,40575138,SRX14566118,SRS12343116,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36642,,0.01834,,0.90709,,0.41421,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69102,SRR20220073,SRX14566118,SRS12343116,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL100,GSM5965371,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL100,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965371,GSM5965371: Micorwell seq datasets of Zebrafish 22m COL100; Danio rerio; RNA Seq,GSM5965371 r1,GSM5965371,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL100_4_2.fq.gz Zebrafish_22m_COL100_4_1.fq.gz,fastq fastq,10839649638.0,124593674.0,GSM5965371 r4,0:24 1:150,A:3647953845;C:2155414977;G:2193427718;T:2815506032;N:27347066,24,150,,,3647953845,2155414977,2193427718,2815506032,27347066,SRX14566118,SRS12343116,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37732,,0.01892,,0.90611,,0.41495,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69103,SRR18432299,SRX14566117,SRS12343115,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL99,GSM5965370,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL99,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965370,GSM5965370: Micorwell seq datasets of Zebrafish 22m COL99; Danio rerio; RNA Seq,GSM5965370 r1,GSM5965370,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL99_1_1.fq.gz Zebrafish_22m_COL99_1_2.fq.gz,fastq fastq,7342361700.0,48949078.0,GSM5965370 r1,0:150 1:150,A:2167085889;C:1328709678;G:1371279362;T:2472729217;N:2557554,150,150,,,2167085889,1328709678,1371279362,2472729217,2557554,SRX14566117,SRS12343115,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35218,,0.02022,,0.88172,,0.40931,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69104,SRR19574841,SRX14566117,SRS12343115,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL99,GSM5965370,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL99,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965370,GSM5965370: Micorwell seq datasets of Zebrafish 22m COL99; Danio rerio; RNA Seq,GSM5965370 r1,GSM5965370,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL99_2_2.fq.gz Zebrafish_22m_COL99_2_1.fq.gz,fastq fastq,23158201260.0,179520940.0,GSM5965370 r2,0:108 1:150,A:6801877664;C:4592887625;G:4915083111;T:6815702760;N:32650100,108,150,,,6801877664,4592887625,4915083111,6815702760,32650100,SRX14566117,SRS12343115,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39104,,0.02058,,0.91378,,0.42997,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69105,SRR19600345,SRX14566117,SRS12343115,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL99,GSM5965370,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL99,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965370,GSM5965370: Micorwell seq datasets of Zebrafish 22m COL99; Danio rerio; RNA Seq,GSM5965370 r1,GSM5965370,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL99_3_1.fq.gz Zebrafish_22m_COL99_3_2.fq.gz,fastq fastq,14305689618.0,164433214.0,GSM5965370 r3,0:24 1:150,A:4861940513;C:2831334489;G:2853025415;T:3704990873;N:54398328,24,150,,,4861940513,2831334489,2853025415,3704990873,54398328,SRX14566117,SRS12343115,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35904,,0.01836,,0.90471,,0.43549,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69106,SRR20220072,SRX14566117,SRS12343115,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL99,GSM5965370,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL99,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965370,GSM5965370: Micorwell seq datasets of Zebrafish 22m COL99; Danio rerio; RNA Seq,GSM5965370 r1,GSM5965370,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL99_4_2.fq.gz Zebrafish_22m_COL99_4_1.fq.gz,fastq fastq,15260086752.0,175403296.0,GSM5965370 r4,0:24 1:150,A:5185321096;C:3015789376;G:3064259416;T:3956859513;N:37857351,24,150,,,5185321096,3015789376,3064259416,3956859513,37857351,SRX14566117,SRS12343115,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36721,,0.01828,,0.90331,,0.43099,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69107,SRR18432300,SRX14566116,SRS12343114,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL98,GSM5965369,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL98,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965369,GSM5965369: Micorwell seq datasets of Zebrafish 22m COL98; Danio rerio; RNA Seq,GSM5965369 r1,GSM5965369,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL98_1_2.fq.gz Zebrafish_22m_COL98_1_1.fq.gz,fastq fastq,5938444500.0,39589630.0,GSM5965369 r1,0:150 1:150,A:1758895503;C:1070256355;G:1106954199;T:2000229880;N:2108563,150,150,,,1758895503,1070256355,1106954199,2000229880,2108563,SRX14566116,SRS12343114,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34396,,0.02144,,0.88732,,0.42814,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69108,SRR19574840,SRX14566116,SRS12343114,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL98,GSM5965369,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL98,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965369,GSM5965369: Micorwell seq datasets of Zebrafish 22m COL98; Danio rerio; RNA Seq,GSM5965369 r1,GSM5965369,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL98_2_2.fq.gz Zebrafish_22m_COL98_2_1.fq.gz,fastq fastq,18950667342.0,146904398.0,GSM5965369 r2,0:108 1:150,A:5563615657;C:3754580615;G:4025718357;T:5579503919;N:27248794,108,150,,,5563615657,3754580615,4025718357,5579503919,27248794,SRX14566116,SRS12343114,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38541,,0.02055,,0.91595,,0.44038,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69109,SRR19600344,SRX14566116,SRS12343114,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL98,GSM5965369,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL98,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965369,GSM5965369: Micorwell seq datasets of Zebrafish 22m COL98; Danio rerio; RNA Seq,GSM5965369 r1,GSM5965369,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL98_3_2.fq.gz Zebrafish_22m_COL98_3_1.fq.gz,fastq fastq,11565622008.0,132938184.0,GSM5965369 r3,0:24 1:150,A:3931052782;C:2290541845;G:2311160387;T:2988933252;N:43933742,24,150,,,3931052782,2290541845,2311160387,2988933252,43933742,SRX14566116,SRS12343114,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35787,,0.01902,,0.90554,,0.44163,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69110,SRR20220071,SRX14566116,SRS12343114,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL98,GSM5965369,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL98,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965369,GSM5965369: Micorwell seq datasets of Zebrafish 22m COL98; Danio rerio; RNA Seq,GSM5965369 r1,GSM5965369,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL98_4_2.fq.gz Zebrafish_22m_COL98_4_1.fq.gz,fastq fastq,12798089412.0,147104476.0,GSM5965369 r4,0:24 1:150,A:4354231302;C:2522847485;G:2575887489;T:3314314332;N:30808804,24,150,,,4354231302,2522847485,2575887489,3314314332,30808804,SRX14566116,SRS12343114,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36534,,0.01997,,0.90599,,0.44153,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69111,SRR18432301,SRX14566115,SRS12343113,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL29,GSM5965368,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL29,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965368,GSM5965368: Micorwell seq datasets of Zebrafish 22m COL29; Danio rerio; RNA Seq,GSM5965368 r1,GSM5965368,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL29_1_2.fq.gz Zebrafish_22m_COL29_1_1.fq.gz,fastq fastq,7581777300.0,50545182.0,GSM5965368 r1,0:150 1:150,A:2250106505;C:1381731283;G:1419439772;T:2527769280;N:2730460,150,150,,,2250106505,1381731283,1419439772,2527769280,2730460,SRX14566115,SRS12343113,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36765,,0.01494,,0.90729,,0.35288,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69112,SRR19368203,SRX14566115,SRS12343113,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL29,GSM5965368,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL29,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965368,GSM5965368: Micorwell seq datasets of Zebrafish 22m COL29; Danio rerio; RNA Seq,GSM5965368 r1,GSM5965368,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL29_2_2.fq.gz Zebrafish_22m_COL29_2_1.fq.gz,fastq fastq,24706758540.0,191525260.0,GSM5965368 r2,0:108 1:150,A:7243835856;C:4912810904;G:5266791629;T:7247039456;N:36280695,108,150,,,7243835856,4912810904,5266791629,7247039456,36280695,SRX14566115,SRS12343113,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.41806,,0.0146,,0.93091,,0.33332,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69113,SRR19600343,SRX14566115,SRS12343113,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL29,GSM5965368,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL29,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965368,GSM5965368: Micorwell seq datasets of Zebrafish 22m COL29; Danio rerio; RNA Seq,GSM5965368 r1,GSM5965368,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL29_3_2.fq.gz Zebrafish_22m_COL29_3_1.fq.gz,fastq fastq,15303263112.0,175899576.0,GSM5965368 r3,0:24 1:150,A:5167675905;C:3018555240;G:3029922145;T:4028679196;N:58430626,24,150,,,5167675905,3018555240,3029922145,4028679196,58430626,SRX14566115,SRS12343113,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38632,,0.01455,,0.92322,,0.34744,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69114,SRR20230006,SRX14566115,SRS12343113,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL29,GSM5965368,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL29,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965368,GSM5965368: Micorwell seq datasets of Zebrafish 22m COL29; Danio rerio; RNA Seq,GSM5965368 r1,GSM5965368,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL29_4_2.fq.gz Zebrafish_22m_COL29_4_1.fq.gz,fastq fastq,17069362416.0,196199568.0,GSM5965368 r4,0:24 1:150,A:5757405783;C:3368033997;G:3400394688;T:4500190805;N:43337143,24,150,,,5757405783,3368033997,3400394688,4500190805,43337143,SRX14566115,SRS12343113,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3939,,0.01427,,0.92287,,0.33699,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69115,SRR18432302,SRX14566114,SRS12343112,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL28,GSM5965367,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL28,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965367,GSM5965367: Micorwell seq datasets of Zebrafish 22m COL28; Danio rerio; RNA Seq,GSM5965367 r1,GSM5965367,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL28_1_1.fq.gz Zebrafish_22m_COL28_1_2.fq.gz,fastq fastq,7826951700.0,52179678.0,GSM5965367 r1,0:150 1:150,A:2323409101;C:1429475496;G:1471378966;T:2599893921;N:2794216,150,150,,,2323409101,1429475496,1471378966,2599893921,2794216,SRX14566114,SRS12343112,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37337,,0.01545,,0.90461,,0.34521,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69116,SRR19368202,SRX14566114,SRS12343112,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL28,GSM5965367,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL28,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965367,GSM5965367: Micorwell seq datasets of Zebrafish 22m COL28; Danio rerio; RNA Seq,GSM5965367 r1,GSM5965367,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL28_2_2.fq.gz Zebrafish_22m_COL28_2_1.fq.gz,fastq fastq,25820087106.0,200155714.0,GSM5965367 r2,0:108 1:150,A:7560770671;C:5174347897;G:5565098094;T:7482492804;N:37377640,108,150,,,7560770671,5174347897,5565098094,7482492804,37377640,SRX14566114,SRS12343112,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.43399,,0.01555,,0.92811,,0.33152,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69117,SRR19600342,SRX14566114,SRS12343112,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL28,GSM5965367,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL28,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965367,GSM5965367: Micorwell seq datasets of Zebrafish 22m COL28; Danio rerio; RNA Seq,GSM5965367 r1,GSM5965367,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL28_3_1.fq.gz Zebrafish_22m_COL28_3_2.fq.gz,fastq fastq,16283222934.0,187163482.0,GSM5965367 r3,0:24 1:150,A:5493743190;C:3233659251;G:3255765506;T:4237980273;N:62074714,24,150,,,5493743190,3233659251,3255765506,4237980273,62074714,SRX14566114,SRS12343112,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39151,,0.01367,,0.92334,,0.33648,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69118,SRR20230005,SRX14566114,SRS12343112,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL28,GSM5965367,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL28,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965367,GSM5965367: Micorwell seq datasets of Zebrafish 22m COL28; Danio rerio; RNA Seq,GSM5965367 r1,GSM5965367,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL28_4_2.fq.gz Zebrafish_22m_COL28_4_1.fq.gz,fastq fastq,16754354556.0,192578788.0,GSM5965367 r4,0:24 1:150,A:5619677705;C:3335915497;G:3373736074;T:4382199390;N:42825890,24,150,,,5619677705,3335915497,3373736074,4382199390,42825890,SRX14566114,SRS12343112,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40455,,0.01479,,0.92149,,0.33527,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69119,SRR18432303,SRX14566113,SRS12343111,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL26,GSM5965366,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL26,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965366,GSM5965366: Micorwell seq datasets of Zebrafish 22m COL26; Danio rerio; RNA Seq,GSM5965366 r1,GSM5965366,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL26_1_2.fq.gz Zebrafish_22m_COL26_1_1.fq.gz,fastq fastq,8146547400.0,54310316.0,GSM5965366 r1,0:150 1:150,A:2416747711;C:1494300256;G:1538832328;T:2693808669;N:2858436,150,150,,,2416747711,1494300256,1538832328,2693808669,2858436,SRX14566113,SRS12343111,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35353,,0.01597,,0.91202,,0.32572,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69120,SRR19368201,SRX14566113,SRS12343111,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL26,GSM5965366,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL26,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965366,GSM5965366: Micorwell seq datasets of Zebrafish 22m COL26; Danio rerio; RNA Seq,GSM5965366 r1,GSM5965366,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL26_2_2.fq.gz Zebrafish_22m_COL26_2_1.fq.gz,fastq fastq,26990221596.0,209226524.0,GSM5965366 r2,0:108 1:150,A:7967360290;C:5377249138;G:5762633566;T:7844513332;N:38465270,108,150,,,7967360290,5377249138,5762633566,7844513332,38465270,SRX14566113,SRS12343111,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39923,,0.01661,,0.93728,,0.31437,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69121,SRR19600341,SRX14566113,SRS12343111,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL26,GSM5965366,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL26,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965366,GSM5965366: Micorwell seq datasets of Zebrafish 22m COL26; Danio rerio; RNA Seq,GSM5965366 r1,GSM5965366,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL26_3_2.fq.gz Zebrafish_22m_COL26_3_1.fq.gz,fastq fastq,16738636962.0,192398126.0,GSM5965366 r3,0:24 1:150,A:5740314808;C:3286765181;G:3307994492;T:4339946982;N:63615499,24,150,,,5740314808,3286765181,3307994492,4339946982,63615499,SRX14566113,SRS12343111,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35598,,0.01478,,0.93332,,0.30927,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69122,SRR20230004,SRX14566113,SRS12343111,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL26,GSM5965366,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL26,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965366,GSM5965366: Micorwell seq datasets of Zebrafish 22m COL26; Danio rerio; RNA Seq,GSM5965366 r1,GSM5965366,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL26_4_1.fq.gz Zebrafish_22m_COL26_4_2.fq.gz,fastq fastq,18291233394.0,210244062.0,GSM5965366 r4,0:24 1:150,A:6252289788;C:3596253868;G:3645465304;T:4750348347;N:46876087,24,150,,,6252289788,3596253868,3645465304,4750348347,46876087,SRX14566113,SRS12343111,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36964,,0.01527,,0.93016,,0.314,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69123,SRR18432304,SRX14566112,SRS12343110,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL25,GSM5965365,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL25,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965365,GSM5965365: Micorwell seq datasets of Zebrafish 22m COL25; Danio rerio; RNA Seq,GSM5965365 r1,GSM5965365,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL25_1_2.fq.gz Zebrafish_22m_COL25_1_1.fq.gz,fastq fastq,7386895500.0,49245970.0,GSM5965365 r1,0:150 1:150,A:2188943122;C:1352466099;G:1391208556;T:2451623671;N:2654052,150,150,,,2188943122,1352466099,1391208556,2451623671,2654052,SRX14566112,SRS12343110,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34829,,0.01702,,0.91011,,0.34696,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69124,SRR19368200,SRX14566112,SRS12343110,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL25,GSM5965365,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL25,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965365,GSM5965365: Micorwell seq datasets of Zebrafish 22m COL25; Danio rerio; RNA Seq,GSM5965365 r1,GSM5965365,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL25_2_1.fq.gz Zebrafish_22m_COL25_2_2.fq.gz,fastq fastq,24439389786.0,189452634.0,GSM5965365 r2,0:108 1:150,A:7206398545;C:4850830421;G:5202414831;T:7143901244;N:35844745,108,150,,,7206398545,4850830421,5202414831,7143901244,35844745,SRX14566112,SRS12343110,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39244,,0.01665,,0.93561,,0.33395,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69125,SRR19600340,SRX14566112,SRS12343110,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL25,GSM5965365,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL25,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965365,GSM5965365: Micorwell seq datasets of Zebrafish 22m COL25; Danio rerio; RNA Seq,GSM5965365 r1,GSM5965365,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL25_3_1.fq.gz Zebrafish_22m_COL25_3_2.fq.gz,fastq fastq,14886524934.0,171109482.0,GSM5965365 r3,0:24 1:150,A:5054066629;C:2935627519;G:2951049142;T:3888081486;N:57700158,24,150,,,5054066629,2935627519,2951049142,3888081486,57700158,SRX14566112,SRS12343110,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35663,,0.01562,,0.92847,,0.32068,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69126,SRR20230003,SRX14566112,SRS12343110,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL25,GSM5965365,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL25,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5965365,GSM5965365: Micorwell seq datasets of Zebrafish 22m COL25; Danio rerio; RNA Seq,GSM5965365 r1,GSM5965365,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL25_4_1.fq.gz Zebrafish_22m_COL25_4_2.fq.gz,fastq fastq,15319397610.0,176085030.0,GSM5965365 r4,0:24 1:150,A:5196794440;C:3025206059;G:3053061397;T:4004012980;N:40322734,24,150,,,5196794440,3025206059,3053061397,4004012980,40322734,SRX14566112,SRS12343110,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36743,,0.01643,,0.92717,,0.33246,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-22,Adult,Adult,Whole Organism,All anatomical structures 69127,SRR18324407,SRX14462008,SRS12265561,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL96,GSM5952449,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL96,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952449,GSM5952449: Micorwell seq datasets of Zebrafish 22m COL96; Danio rerio; RNA Seq,GSM5952449 r1,GSM5952449,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL96_1_1.fq.gz Zebrafish_22m_COL96_1_2.fq.gz,fastq fastq,7585326300.0,50568842.0,GSM5952449 r1,0:150 1:150,A:2222934338;C:1372003512;G:1421274760;T:2566437144;N:2676546,150,150,,,2222934338,1372003512,1421274760,2566437144,2676546,SRX14462008,SRS12265561,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36472,,0.02138,,0.87903,,0.40976,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69128,SRR19574838,SRX14462008,SRS12265561,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL96,GSM5952449,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL96,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952449,GSM5952449: Micorwell seq datasets of Zebrafish 22m COL96; Danio rerio; RNA Seq,GSM5952449 r1,GSM5952449,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL96_2_1.fq.gz Zebrafish_22m_COL96_2_2.fq.gz,fastq fastq,23678760378.0,183556282.0,GSM5952449 r2,0:108 1:150,A:6835986863;C:4754567504;G:5117713497;T:6935921626;N:34570888,108,150,,,6835986863,4754567504,5117713497,6935921626,34570888,SRX14462008,SRS12265561,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.42365,,0.02178,,0.90808,,0.42539,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69129,SRR19600334,SRX14462008,SRS12265561,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL96,GSM5952449,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL96,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952449,GSM5952449: Micorwell seq datasets of Zebrafish 22m COL96; Danio rerio; RNA Seq,GSM5952449 r1,GSM5952449,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL96_3_1.fq.gz Zebrafish_22m_COL96_3_2.fq.gz,fastq fastq,14446071774.0,166046802.0,GSM5952449 r3,0:24 1:150,A:4762589459;C:2903954370;G:2949658398;T:3775118427;N:54751120,24,150,,,4762589459,2903954370,2949658398,3775118427,54751120,SRX14462008,SRS12265561,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39057,,0.01981,,0.89706,,0.42859,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69130,SRR20220069,SRX14462008,SRS12265561,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL96,GSM5952449,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL96,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952449,GSM5952449: Micorwell seq datasets of Zebrafish 22m COL96; Danio rerio; RNA Seq,GSM5952449 r1,GSM5952449,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL96_4_1.fq.gz Zebrafish_22m_COL96_4_2.fq.gz,fastq fastq,16164846036.0,185802828.0,GSM5952449 r4,0:24 1:150,A:5323547808;C:3234690319;G:3319094681;T:4250240266;N:37272962,24,150,,,5323547808,3234690319,3319094681,4250240266,37272962,SRX14462008,SRS12265561,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39781,,0.02136,,0.89542,,0.4178,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69131,SRR18324408,SRX14462007,SRS12265560,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL97,GSM5952450,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL97,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952450,GSM5952450: Micorwell seq datasets of Zebrafish 22m COL97; Danio rerio; RNA Seq,GSM5952450 r1,GSM5952450,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL97_1_1.fq.gz Zebrafish_22m_COL97_1_2.fq.gz,fastq fastq,7247019000.0,48313460.0,GSM5952450 r1,0:150 1:150,A:2121610220;C:1321764255;G:1366953984;T:2434135976;N:2554565,150,150,,,2121610220,1321764255,1366953984,2434135976,2554565,SRX14462007,SRS12265560,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36832,,0.0208,,0.87939,,0.42824,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69132,SRR19574839,SRX14462007,SRS12265560,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL97,GSM5952450,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL97,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952450,GSM5952450: Micorwell seq datasets of Zebrafish 22m COL97; Danio rerio; RNA Seq,GSM5952450 r1,GSM5952450,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL97_2_1.fq.gz Zebrafish_22m_COL97_2_2.fq.gz,fastq fastq,24817186410.0,192381290.0,GSM5952450 r2,0:108 1:150,A:7187812878;C:4969274402;G:5339518780;T:7284148860;N:36431490,108,150,,,7187812878,4969274402,5339518780,7284148860,36431490,SRX14462007,SRS12265560,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.4258,,0.02202,,0.90978,,0.40966,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69133,SRR19600335,SRX14462007,SRS12265560,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL97,GSM5952450,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL97,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952450,GSM5952450: Micorwell seq datasets of Zebrafish 22m COL97; Danio rerio; RNA Seq,GSM5952450 r1,GSM5952450,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL97_3_1.fq.gz Zebrafish_22m_COL97_3_2.fq.gz,fastq fastq,16274464122.0,187062806.0,GSM5952450 r3,0:24 1:150,A:5528818880;C:3201044823;G:3221013048;T:4262149376;N:61437995,24,150,,,5528818880,3201044823,3221013048,4262149376,61437995,SRX14462007,SRS12265560,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37883,,0.01979,,0.90483,,0.42056,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69134,SRR20220070,SRX14462007,SRS12265560,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL97,GSM5952450,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL97,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952450,GSM5952450: Micorwell seq datasets of Zebrafish 22m COL97; Danio rerio; RNA Seq,GSM5952450 r1,GSM5952450,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL97_4_1.fq.gz Zebrafish_22m_COL97_4_2.fq.gz,fastq fastq,17053653000.0,196019000.0,GSM5952450 r4,0:24 1:150,A:5744300088;C:3373489093;G:3418764682;T:4475792525;N:41306612,24,150,,,5744300088,3373489093,3418764682,4475792525,41306612,SRX14462007,SRS12265560,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39497,,0.02031,,0.90327,,0.41726,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69135,SRR18324409,SRX14462006,SRS12265559,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL85,GSM5952438,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL85,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952438,GSM5952438: Micorwell seq datasets of Zebrafish 22m COL85; Danio rerio; RNA Seq,GSM5952438 r1,GSM5952438,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL85_1_1.fq.gz Zebrafish_22m_COL85_1_2.fq.gz,fastq fastq,6413133900.0,42754226.0,GSM5952438 r1,0:150 1:150,A:1897367251;C:1147604565;G:1183651417;T:2182187144;N:2323523,150,150,,,1897367251,1147604565,1183651417,2182187144,2323523,SRX14462006,SRS12265559,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.34444,,0.01887,,0.87539,,0.5329,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69136,SRR19574827,SRX14462006,SRS12265559,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL85,GSM5952438,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL85,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952438,GSM5952438: Micorwell seq datasets of Zebrafish 22m COL85; Danio rerio; RNA Seq,GSM5952438 r1,GSM5952438,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL85_2_2.fq.gz Zebrafish_22m_COL85_2_1.fq.gz,fastq fastq,20982367806.0,162654014.0,GSM5952438 r2,0:108 1:150,A:6145740316;C:4134190174;G:4430830902;T:6241336193;N:30270221,108,150,,,6145740316,4134190174,4430830902,6241336193,30270221,SRX14462006,SRS12265559,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39587,,0.02024,,0.90368,,0.52839,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69137,SRR19600323,SRX14462006,SRS12265559,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL85,GSM5952438,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL85,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952438,GSM5952438: Micorwell seq datasets of Zebrafish 22m COL85; Danio rerio; RNA Seq,GSM5952438 r1,GSM5952438,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL85_3_2.fq.gz Zebrafish_22m_COL85_3_1.fq.gz,fastq fastq,13536198804.0,155588492.0,GSM5952438 r3,0:24 1:150,A:4632670200;C:2642882787;G:2645581540;T:3563693787;N:51370490,24,150,,,4632670200,2642882787,2645581540,3563693787,51370490,SRX14462006,SRS12265559,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36174,,0.01851,,0.89613,,0.53686,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69138,SRR20220058,SRX14462006,SRS12265559,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL85,GSM5952438,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL85,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952438,GSM5952438: Micorwell seq datasets of Zebrafish 22m COL85; Danio rerio; RNA Seq,GSM5952438 r1,GSM5952438,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL85_4_2.fq.gz Zebrafish_22m_COL85_4_1.fq.gz,fastq fastq,13825697916.0,158916068.0,GSM5952438 r4,0:24 1:150,A:4698178869;C:2709915600;G:2736517029;T:3646324015;N:34762403,24,150,,,4698178869,2709915600,2736517029,3646324015,34762403,SRX14462006,SRS12265559,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37421,,0.01894,,0.89467,,0.50407,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69139,SRR18324410,SRX14462005,SRS12265558,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL84,GSM5952437,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL84,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952437,GSM5952437: Micorwell seq datasets of Zebrafish 22m COL84; Danio rerio; RNA Seq,GSM5952437 r1,GSM5952437,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL84_1_1.fq.gz Zebrafish_22m_COL84_1_2.fq.gz,fastq fastq,6338504100.0,42256694.0,GSM5952437 r1,0:150 1:150,A:1867231220;C:1134885370;G:1175142881;T:2158934330;N:2310299,150,150,,,1867231220,1134885370,1175142881,2158934330,2310299,SRX14462005,SRS12265558,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.33913,,0.03324,,0.8574,,0.52545,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69140,SRR19574826,SRX14462005,SRS12265558,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL84,GSM5952437,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL84,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952437,GSM5952437: Micorwell seq datasets of Zebrafish 22m COL84; Danio rerio; RNA Seq,GSM5952437 r1,GSM5952437,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL84_2_1.fq.gz Zebrafish_22m_COL84_2_2.fq.gz,fastq fastq,20819585286.0,161392134.0,GSM5952437 r2,0:108 1:150,A:6098775824;C:4097294841;G:4406784428;T:6186205144;N:30525049,108,150,,,6098775824,4097294841,4406784428,6186205144,30525049,SRX14462005,SRS12265558,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.38186,,0.03663,,0.88887,,0.52697,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69141,SRR19600322,SRX14462005,SRS12265558,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL84,GSM5952437,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL84,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952437,GSM5952437: Micorwell seq datasets of Zebrafish 22m COL84; Danio rerio; RNA Seq,GSM5952437 r1,GSM5952437,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL84_3_1.fq.gz Zebrafish_22m_COL84_3_2.fq.gz,fastq fastq,12734377920.0,146372160.0,GSM5952437 r3,0:24 1:150,A:4285909304;C:2507360964;G:2534958626;T:3357178762;N:48970264,24,150,,,4285909304,2507360964,2534958626,3357178762,48970264,SRX14462005,SRS12265558,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35827,,0.0332,,0.87545,,0.50564,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69142,SRR20220057,SRX14462005,SRS12265558,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL84,GSM5952437,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL84,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952437,GSM5952437: Micorwell seq datasets of Zebrafish 22m COL84; Danio rerio; RNA Seq,GSM5952437 r1,GSM5952437,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL84_4_1.fq.gz Zebrafish_22m_COL84_4_2.fq.gz,fastq fastq,12215026722.0,140402606.0,GSM5952437 r4,0:24 1:150,A:4110444308;C:2397992865;G:2445036392;T:3230623394;N:30929763,24,150,,,4110444308,2397992865,2445036392,3230623394,30929763,SRX14462005,SRS12265558,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36695,,0.03391,,0.87584,,0.52516,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69143,SRR18324411,SRX14462004,SRS12265556,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL95,GSM5952448,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL95,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952448,GSM5952448: Micorwell seq datasets of Zebrafish 22m COL95; Danio rerio; RNA Seq,GSM5952448 r1,GSM5952448,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL95_1_1.fq.gz Zebrafish_22m_COL95_1_2.fq.gz,fastq fastq,7693641600.0,51290944.0,GSM5952448 r1,0:150 1:150,A:2272261425;C:1389032623;G:1435188830;T:2594395740;N:2762982,150,150,,,2272261425,1389032623,1435188830,2594395740,2762982,SRX14462004,SRS12265556,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.35258,,0.02004,,0.88428,,0.44102,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69144,SRR19574837,SRX14462004,SRS12265556,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL95,GSM5952448,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL95,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952448,GSM5952448: Micorwell seq datasets of Zebrafish 22m COL95; Danio rerio; RNA Seq,GSM5952448 r1,GSM5952448,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL95_2_1.fq.gz Zebrafish_22m_COL95_2_2.fq.gz,fastq fastq,24591374748.0,190630812.0,GSM5952448 r2,0:108 1:150,A:7205233879;C:4874896710;G:5224131481;T:7251767536;N:35345142,108,150,,,7205233879,4874896710,5224131481,7251767536,35345142,SRX14462004,SRS12265556,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.40403,,0.02102,,0.91224,,0.43452,,108,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69145,SRR19600333,SRX14462004,SRS12265556,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL95,GSM5952448,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL95,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952448,GSM5952448: Micorwell seq datasets of Zebrafish 22m COL95; Danio rerio; RNA Seq,GSM5952448 r1,GSM5952448,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL95_3_1.fq.gz Zebrafish_22m_COL95_3_2.fq.gz,fastq fastq,15781039098.0,181391254.0,GSM5952448 r3,0:24 1:150,A:5378282765;C:3100317928;G:3116256783;T:4125933839;N:60247783,24,150,,,5378282765,3100317928,3116256783,4125933839,60247783,SRX14462004,SRS12265556,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36782,,0.01849,,0.90274,,0.44083,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69146,SRR20220068,SRX14462004,SRS12265556,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL95,GSM5952448,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL95,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952448,GSM5952448: Micorwell seq datasets of Zebrafish 22m COL95; Danio rerio; RNA Seq,GSM5952448 r1,GSM5952448,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL95_4_1.fq.gz Zebrafish_22m_COL95_4_2.fq.gz,fastq fastq,16836509526.0,193523098.0,GSM5952448 r4,0:24 1:150,A:5726465059;C:3309296081;G:3359110449;T:4398601627;N:43036310,24,150,,,5726465059,3309296081,3359110449,4398601627,43036310,SRX14462004,SRS12265556,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.37664,,0.01944,,0.90394,,0.44126,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69147,SRR18324412,SRX14462003,SRS12265555,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL94,GSM5952447,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL94,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952447,GSM5952447: Micorwell seq datasets of Zebrafish 22m COL94; Danio rerio; RNA Seq,GSM5952447 r1,GSM5952447,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL94_1_1.fq.gz Zebrafish_22m_COL94_1_2.fq.gz,fastq fastq,6437998800.0,42919992.0,GSM5952447 r1,0:150 1:150,A:1887734041;C:1174667392;G:1212310918;T:2160980327;N:2306122,150,150,,,1887734041,1174667392,1212310918,2160980327,2306122,SRX14462003,SRS12265555,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.36631,,0.02239,,0.87866,,0.42174,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69148,SRR19574836,SRX14462003,SRS12265555,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL94,GSM5952447,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL94,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952447,GSM5952447: Micorwell seq datasets of Zebrafish 22m COL94; Danio rerio; RNA Seq,GSM5952447 r1,GSM5952447,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL94_2_1.fq.gz Zebrafish_22m_COL94_2_2.fq.gz,fastq fastq,22167919860.0,171844340.0,GSM5952447 r2,0:108 1:150,A:6436679704;C:4437403667;G:4762582013;T:6498826164;N:32428312,108,150,,,6436679704,4437403667,4762582013,6498826164,32428312,SRX14462003,SRS12265555,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.41932,,0.02323,,0.90761,,0.41207,,150,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69149,SRR19600332,SRX14462003,SRS12265555,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL94,GSM5952447,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL94,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952447,GSM5952447: Micorwell seq datasets of Zebrafish 22m COL94; Danio rerio; RNA Seq,GSM5952447 r1,GSM5952447,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL94_3_1.fq.gz Zebrafish_22m_COL94_3_2.fq.gz,fastq fastq,14411764194.0,165652462.0,GSM5952447 r3,0:24 1:150,A:4866084703;C:2862523421;G:2873575717;T:3754781896;N:54798457,24,150,,,4866084703,2862523421,2873575717,3754781896,54798457,SRX14462003,SRS12265555,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.3776,,0.02056,,0.90116,,0.414,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures 69150,SRR20220067,SRX14462003,SRS12265555,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 22m COL94,GSM5952447,,source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism,Micorwell seq datasets of Zebrafish 22m COL94,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 1 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. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 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. Assembly: 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 22m sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:22 month|tissue:whole organism,GSM5952447,GSM5952447: Micorwell seq datasets of Zebrafish 22m COL94; Danio rerio; RNA Seq,GSM5952447 r1,GSM5952447,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-T7,,SRP363983,,,Zebrafish_22m_COL94_4_1.fq.gz Zebrafish_22m_COL94_4_2.fq.gz,fastq fastq,13331610996.0,153236908.0,GSM5952447 r4,0:24 1:150,A:4477401580;C:2653158757;G:2685291945;T:3482036534;N:33722180,24,150,,,4477401580,2653158757,2685291945,3482036534,33722180,SRX14462003,SRS12265555,SRA1461257,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",1,0.39161,,0.02171,,0.89846,,0.40245,,24,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-14,Adult,Adult,Whole Organism,All anatomical structures