{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Adult\" and technology = \"microwellseq\"", "rows": [[64538, "SRR14915030", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_1_1.fq.gz Zebrafish_3m_COL64_1_2.fq.gz", "fastq fastq", 3509355300.0, 23395702.0, "GSM5400025 r1", "0:150 1:150", "A:1033838372;C:621125453;G:637527732;T:1213662404;N:3201339", 150, 150, null, null, 1033838372, 621125453, 637527732, 1213662404, 3201339, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36321, null, 0.02305, null, 0.82554, null, 0.50827, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64539, "SRR14915031", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_2_1.fq.gz Zebrafish_3m_COL64_2_2.fq.gz", "fastq fastq", 1665060900.0, 11100406.0, "GSM5400025 r2", "0:150 1:150", "A:462369470;C:317060096;G:327014453;T:557786784;N:830097", 150, 150, null, null, 462369470, 317060096, 327014453, 557786784, 830097, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13839, null, 0.00808, null, 0.91569, null, 0.53255, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64540, "SRR14915032", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_3_1.fq.gz Zebrafish_3m_COL64_3_2.fq.gz", "fastq fastq", 2150244600.0, 14334964.0, "GSM5400025 r3", "0:150 1:150", "A:601841098;C:403651653;G:418726941;T:723163387;N:2861521", 150, 150, null, null, 601841098, 403651653, 418726941, 723163387, 2861521, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14947, null, 0.00856, null, 0.91563, null, 0.52901, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64541, "SRR14915033", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_4_1.fq.gz Zebrafish_3m_COL64_4_2.fq.gz", "fastq fastq", 2197416600.0, 14649444.0, "GSM5400025 r4", "0:150 1:150", "A:623049639;C:408736499;G:423211202;T:740201304;N:2217956", 150, 150, null, null, 623049639, 408736499, 423211202, 740201304, 2217956, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.31503, null, 0.01599, null, 0.86805, null, 0.52639, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64542, "SRR14915034", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_5_1.fq.gz Zebrafish_3m_COL64_5_2.fq.gz", "fastq fastq", 15591467400.0, 103943116.0, "GSM5400025 r5", "0:150 1:150", "A:4293072963;C:3172864759;G:3328412245;T:4775949229;N:21168204", 150, 150, null, null, 4293072963, 3172864759, 3328412245, 4775949229, 21168204, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42792, null, 0.02171, null, 0.85798, null, 0.53122, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64543, "SRR14915035", "SRX11229465", "SRS9283357", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL64", "GSM5400025", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL64", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400025", "GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq", "GSM5400025", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL64_6_1.fq.gz Zebrafish_3m_COL64_6_2.fq.gz", "fastq fastq", 12549507270.0, 144247210.0, "GSM5400025 r6", "0:24 1:150", "A:4029002995;C:2554410310;G:2623555177;T:3319223578;N:23315210", 24, 150, null, null, 4029002995, 2554410310, 2623555177, 3319223578, 23315210, "SRX11229465", "SRS9283357", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.38859, null, 0.01815, null, 0.85269, null, 0.5308, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64544, "SRR14915024", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_1_1.fq.gz Zebrafish_3m_COL63_1_2.fq.gz", "fastq fastq", 2055042600.0, 13700284.0, "GSM5400024 r1", "0:150 1:150", "A:611481772;C:368434834;G:377372486;T:695791152;N:1962356", 150, 150, null, null, 611481772, 368434834, 377372486, 695791152, 1962356, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.34483, null, 0.02058, null, 0.82974, null, 0.52413, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64545, "SRR14915025", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_2_1.fq.gz Zebrafish_3m_COL63_2_2.fq.gz", "fastq fastq", 160975800.0, 1073172.0, "GSM5400024 r2", "0:150 1:150", "A:44979062;C:31715522;G:32816505;T:51394061;N:70650", 150, 150, null, null, 44979062, 31715522, 32816505, 51394061, 70650, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14018, null, 0.00811, null, 0.91565, null, 0.53293, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64546, "SRR14915026", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_3_1.fq.gz Zebrafish_3m_COL63_3_2.fq.gz", "fastq fastq", 948599100.0, 6323994.0, "GSM5400024 r3", "0:150 1:150", "A:270719772;C:179859378;G:186167273;T:310493229;N:1359448", 150, 150, null, null, 270719772, 179859378, 186167273, 310493229, 1359448, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15861, null, 0.00833, null, 0.90536, null, 0.53615, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64547, "SRR14915027", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_4_1.fq.gz Zebrafish_3m_COL63_4_2.fq.gz", "fastq fastq", 1296727200.0, 8644848.0, "GSM5400024 r4", "0:150 1:150", "A:373182160;C:244740194;G:252531468;T:424978804;N:1294574", 150, 150, null, null, 373182160, 244740194, 252531468, 424978804, 1294574, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30429, null, 0.0152, null, 0.86466, null, 0.53074, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64548, "SRR14915028", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_5_1.fq.gz Zebrafish_3m_COL63_5_2.fq.gz", "fastq fastq", 7785040500.0, 51900270.0, "GSM5400024 r5", "0:150 1:150", "A:2174090918;C:1597924965;G:1665177229;T:2337394238;N:10453150", 150, 150, null, null, 2174090918, 1597924965, 1665177229, 2337394238, 10453150, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.41787, null, 0.01939, null, 0.85403, null, 0.5287, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64549, "SRR14915029", "SRX11229464", "SRS9283356", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL63", "GSM5400024", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL63", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400024", "GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq", "GSM5400024", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL63_6_1.fq.gz Zebrafish_3m_COL63_6_2.fq.gz", "fastq fastq", 5937968196.0, 68252508.0, "GSM5400024 r6", "0:24 1:150", "A:1934581537;C:1211880492;G:1231715977;T:1548193534;N:11596656", 24, 150, null, null, 1934581537, 1211880492, 1231715977, 1548193534, 11596656, "SRX11229464", "SRS9283356", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37443, null, 0.0171, null, 0.85352, null, 0.52813, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64550, "SRR14915018", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_1_1.fq.gz Zebrafish_3m_COL62_1_2.fq.gz", "fastq fastq", 1789905600.0, 11932704.0, "GSM5400023 r1", "0:150 1:150", "A:537842325;C:316956626;G:324348756;T:609120570;N:1637323", 150, 150, null, null, 537842325, 316956626, 324348756, 609120570, 1637323, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.33127, null, 0.02101, null, 0.84187, null, 0.5271, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64551, "SRR14915019", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_2_1.fq.gz Zebrafish_3m_COL62_2_2.fq.gz", "fastq fastq", 1289058300.0, 8593722.0, "GSM5400023 r2", "0:150 1:150", "A:365275974;C:247054954;G:250766392;T:425210421;N:750559", 150, 150, null, null, 365275974, 247054954, 250766392, 425210421, 750559, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.11204, null, 0.00628, null, 0.92967, null, 0.53143, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64552, "SRR14915020", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_3_1.fq.gz Zebrafish_3m_COL62_3_2.fq.gz", "fastq fastq", 1468221600.0, 9788144.0, "GSM5400023 r3", "0:150 1:150", "A:422901616;C:273721436;G:280933485;T:488734495;N:1930568", 150, 150, null, null, 422901616, 273721436, 280933485, 488734495, 1930568, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13434, null, 0.00748, null, 0.92383, null, 0.53386, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64553, "SRR14915021", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_4_1.fq.gz Zebrafish_3m_COL62_4_2.fq.gz", "fastq fastq", 1551007800.0, 10340052.0, "GSM5400023 r4", "0:150 1:150", "A:450556375;C:286977972;G:294533181;T:517371969;N:1568303", 150, 150, null, null, 450556375, 286977972, 294533181, 517371969, 1568303, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.27413, null, 0.01353, null, 0.88065, null, 0.5239, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64554, "SRR14915022", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_5_1.fq.gz Zebrafish_3m_COL62_5_2.fq.gz", "fastq fastq", 8141951700.0, 54279678.0, "GSM5400023 r5", "0:150 1:150", "A:2279713850;C:1655964521;G:1727447219;T:2467915358;N:10910752", 150, 150, null, null, 2279713850, 1655964521, 1727447219, 2467915358, 10910752, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.40205, null, 0.02062, null, 0.86571, null, 0.53401, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64555, "SRR14915023", "SRX11229463", "SRS9283353", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL62", "GSM5400023", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL62", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400023", "GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq", "GSM5400023", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL62_6_1.fq.gz Zebrafish_3m_COL62_6_2.fq.gz", "fastq fastq", 6366133998.0, 73173954.0, "GSM5400023 r6", "0:24 1:150", "A:2133593269;C:1284155615;G:1311954143;T:1624544767;N:11886204", 24, 150, null, null, 2133593269, 1284155615, 1311954143, 1624544767, 11886204, "SRX11229463", "SRS9283353", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.3596, null, 0.01726, null, 0.86519, null, 0.50248, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64556, "SRR14915012", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_1_1.fq.gz Zebrafish_3m_COL61_1_2.fq.gz", "fastq fastq", 4243314900.0, 28288766.0, "GSM5400022 r1", "0:150 1:150", "A:1245557842;C:757040428;G:775787197;T:1461026513;N:3902920", 150, 150, null, null, 1245557842, 757040428, 775787197, 1461026513, 3902920, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37049, null, 0.02368, null, 0.82613, null, 0.52976, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64557, "SRR14915013", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_2_1.fq.gz Zebrafish_3m_COL61_2_2.fq.gz", "fastq fastq", 1240206900.0, 8268046.0, "GSM5400022 r2", "0:150 1:150", "A:342697940;C:238587916;G:245987086;T:412298823;N:635135", 150, 150, null, null, 342697940, 238587916, 245987086, 412298823, 635135, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13399, null, 0.008, null, 0.9181, null, 0.52385, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64558, "SRR14915014", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_3_1.fq.gz Zebrafish_3m_COL61_3_2.fq.gz", "fastq fastq", 1347541200.0, 8983608.0, "GSM5400022 r3", "0:150 1:150", "A:378035707;C:253070106;G:262848999;T:451676944;N:1909444", 150, 150, null, null, 378035707, 253070106, 262848999, 451676944, 1909444, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.16482, null, 0.00934, null, 0.90414, null, 0.54039, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64559, "SRR14915015", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_4_1.fq.gz Zebrafish_3m_COL61_4_2.fq.gz", "fastq fastq", 2103237600.0, 14021584.0, "GSM5400022 r4", "0:150 1:150", "A:595972315;C:392671732;G:407063253;T:705390065;N:2140235", 150, 150, null, null, 595972315, 392671732, 407063253, 705390065, 2140235, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.32134, null, 0.01649, null, 0.86316, null, 0.49587, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64560, "SRR14915016", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_5_1.fq.gz Zebrafish_3m_COL61_5_2.fq.gz", "fastq fastq", 19534617300.0, 130230782.0, "GSM5400022 r5", "0:150 1:150", "A:5361819748;C:3997534297;G:4189722611;T:5957688281;N:27852363", 150, 150, null, null, 5361819748, 3997534297, 4189722611, 5957688281, 27852363, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.43627, null, 0.02217, null, 0.85693, null, 0.53022, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64561, "SRR14915017", "SRX11229462", "SRS9283355", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL61", "GSM5400022", null, "source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m COL61", "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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400022", "GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq", "GSM5400022", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL61_6_1.fq.gz Zebrafish_3m_COL61_6_2.fq.gz", "fastq fastq", 15060602538.0, 173110374.0, "GSM5400022 r6", "0:24 1:150", "A:4814003802;C:3077509029;G:3135215248;T:4005264504;N:28609955", 24, 150, null, null, 4814003802, 3077509029, 3135215248, 4005264504, 28609955, "SRX11229462", "SRS9283355", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.39158, null, 0.01982, null, 0.85348, null, 0.51089, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64562, "SRR14915286", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_1_1.fq.gz Zebrafish_3m_COL128_1_2.fq.gz", "fastq fastq", 3208770600.0, 21391804.0, "GSM5400069 r1", "0:150 1:150", "A:945845308;C:569438484;G:585368535;T:1105095075;N:3023198", 150, 150, null, null, 945845308, 569438484, 585368535, 1105095075, 3023198, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.3414, null, 0.02928, null, 0.85021, null, 0.51782, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64563, "SRR14915287", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_2_1.fq.gz Zebrafish_3m_COL128_2_2.fq.gz", "fastq fastq", 304801800.0, 2032012.0, "GSM5400069 r2", "0:150 1:150", "A:84325161;C:57825170;G:60519262;T:102006710;N:125497", 150, 150, null, null, 84325161, 57825170, 60519262, 102006710, 125497, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14941, null, 0.01173, null, 0.92151, null, 0.54623, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64564, "SRR14915288", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_3_1.fq.gz Zebrafish_3m_COL128_3_2.fq.gz", "fastq fastq", 1191613200.0, 7944088.0, "GSM5400069 r3", "0:150 1:150", "A:334533793;C:224286886;G:233943665;T:397197115;N:1651741", 150, 150, null, null, 334533793, 224286886, 233943665, 397197115, 1651741, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15569, null, 0.0115, null, 0.9207, null, 0.54743, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64565, "SRR14915289", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_4_1.fq.gz Zebrafish_3m_COL128_4_2.fq.gz", "fastq fastq", 1766814000.0, 11778760.0, "GSM5400069 r4", "0:150 1:150", "A:500417014;C:333000747;G:344717291;T:586926285;N:1752663", 150, 150, null, null, 500417014, 333000747, 344717291, 586926285, 1752663, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.29677, null, 0.01992, null, 0.88645, null, 0.54665, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64566, "SRR14915290", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_5_1.fq.gz Zebrafish_3m_COL128_5_2.fq.gz", "fastq fastq", 15144379800.0, 100962532.0, "GSM5400069 r5", "0:150 1:150", "A:4075035270;C:3166217509;G:3409509586;T:4473533042;N:20084393", 150, 150, null, null, 4075035270, 3166217509, 3409509586, 4473533042, 20084393, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37107, null, 0.02472, null, 0.88509, null, 0.54349, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64567, "SRR14915291", "SRX11229461", "SRS9283354", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL128", "GSM5400069", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400069", "GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq", "GSM5400069", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL128_6_1.fq.gz Zebrafish_3m_COL128_6_2.fq.gz", "fastq fastq", 11721521832.0, 134730136.0, "GSM5400069 r6", "0:24 1:150", "A:3640769264;C:2518212610;G:2406793302;T:3133328455;N:22418201", 24, 150, null, null, 3640769264, 2518212610, 2406793302, 3133328455, 22418201, "SRX11229461", "SRS9283354", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.34007, null, 0.02128, null, 0.88032, null, 0.54961, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64568, "SRR14915280", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_1_1.fq.gz Zebrafish_3m_COL127_1_2.fq.gz", "fastq fastq", 2746310400.0, 18308736.0, "GSM5400068 r1", "0:150 1:150", "A:806781242;C:487253172;G:500916690;T:948772411;N:2586885", 150, 150, null, null, 806781242, 487253172, 500916690, 948772411, 2586885, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36116, null, 0.03633, null, 0.84587, null, 0.53626, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64569, "SRR14915281", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_2_1.fq.gz Zebrafish_3m_COL127_2_2.fq.gz", "fastq fastq", 1701404100.0, 11342694.0, "GSM5400068 r2", "0:150 1:150", "A:469834000;C:332532377;G:339422396;T:558600197;N:1015130", 150, 150, null, null, 469834000, 332532377, 339422396, 558600197, 1015130, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.1265, null, 0.01237, null, 0.93152, null, 0.53316, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64570, "SRR14915282", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_3_1.fq.gz Zebrafish_3m_COL127_3_2.fq.gz", "fastq fastq", 1339582500.0, 8930550.0, "GSM5400068 r3", "0:150 1:150", "A:374492185;C:255730803;G:264255158;T:443331862;N:1772492", 150, 150, null, null, 374492185, 255730803, 264255158, 443331862, 1772492, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15302, null, 0.01389, null, 0.9236, null, 0.52455, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64571, "SRR14915283", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_4_1.fq.gz Zebrafish_3m_COL127_4_2.fq.gz", "fastq fastq", 1367540100.0, 9116934.0, "GSM5400068 r4", "0:150 1:150", "A:387379474;C:258496197;G:266901212;T:453386759;N:1376458", 150, 150, null, null, 387379474, 258496197, 266901212, 453386759, 1376458, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.32389, null, 0.02782, null, 0.87913, null, 0.53804, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64572, "SRR14915284", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_5_1.fq.gz Zebrafish_3m_COL127_5_2.fq.gz", "fastq fastq", 10892960400.0, 72619736.0, "GSM5400068 r5", "0:150 1:150", "A:3010970636;C:2227858579;G:2327578951;T:3312264759;N:14287475", 150, 150, null, null, 3010970636, 2227858579, 2327578951, 3312264759, 14287475, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.41723, null, 0.03455, null, 0.87345, null, 0.53603, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64573, "SRR14915285", "SRX11229460", "SRS9289443", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL127", "GSM5400068", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400068", "GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq", "GSM5400068", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL127_6_1.fq.gz Zebrafish_3m_COL127_6_2.fq.gz", "fastq fastq", 8590523028.0, 98741644.0, "GSM5400068 r6", "0:24 1:150", "A:2744332263;C:1751755618;G:1790836239;T:2287153559;N:16445349", 24, 150, null, null, 2744332263, 1751755618, 1790836239, 2287153559, 16445349, "SRX11229460", "SRS9289443", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37598, null, 0.02831, null, 0.87028, null, 0.53692, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64574, "SRR14915274", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_1_1.fq.gz Zebrafish_3m_COL126_1_2.fq.gz", "fastq fastq", 3367480500.0, 22449870.0, "GSM5400067 r1", "0:150 1:150", "A:988357060;C:594065773;G:612600123;T:1169171017;N:3286527", 150, 150, null, null, 988357060, 594065773, 612600123, 1169171017, 3286527, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36442, null, 0.03788, null, 0.83707, null, 0.53153, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64575, "SRR14915275", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_2_1.fq.gz Zebrafish_3m_COL126_2_2.fq.gz", "fastq fastq", 2217890100.0, 14785934.0, "GSM5400067 r2", "0:150 1:150", "A:611233800;C:426890176;G:440427980;T:738097977;N:1240167", 150, 150, null, null, 611233800, 426890176, 440427980, 738097977, 1240167, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13061, null, 0.01274, null, 0.92186, null, 0.52329, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64576, "SRR14915276", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_3_1.fq.gz Zebrafish_3m_COL126_3_2.fq.gz", "fastq fastq", 2127274200.0, 14181828.0, "GSM5400067 r3", "0:150 1:150", "A:592506103;C:401844212;G:419018214;T:711110076;N:2795595", 150, 150, null, null, 592506103, 401844212, 419018214, 711110076, 2795595, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15085, null, 0.01391, null, 0.91912, null, 0.50158, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64577, "SRR14915277", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_4_1.fq.gz Zebrafish_3m_COL126_4_2.fq.gz", "fastq fastq", 2170011000.0, 14466740.0, "GSM5400067 r4", "0:150 1:150", "A:612178252;C:405838172;G:422117791;T:727705097;N:2171688", 150, 150, null, null, 612178252, 405838172, 422117791, 727705097, 2171688, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.31735, null, 0.02846, null, 0.87111, null, 0.51932, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64578, "SRR14915278", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_5_2.fq.gz Zebrafish_3m_COL126_5_1.fq.gz", "fastq fastq", 12412172700.0, 82747818.0, "GSM5400067 r5", "0:150 1:150", "A:3428337367;C:2521025487;G:2650242372;T:3796533380;N:16034094", 150, 150, null, null, 3428337367, 2521025487, 2650242372, 3796533380, 16034094, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.422, null, 0.03542, null, 0.8661, null, 0.54056, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64579, "SRR14915279", "SRX11229459", "SRS9283351", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL126", "GSM5400067", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400067", "GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq", "GSM5400067", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL126_6_1.fq.gz Zebrafish_3m_COL126_6_2.fq.gz", "fastq fastq", 10084544970.0, 115914310.0, "GSM5400067 r6", "0:24 1:150", "A:3246792678;C:2042678037;G:2092562882;T:2683662920;N:18848453", 24, 150, null, null, 3246792678, 2042678037, 2092562882, 2683662920, 18848453, "SRX11229459", "SRS9283351", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.3807, null, 0.03251, null, 0.86726, null, 0.53521, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64580, "SRR14915268", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_1_1.fq.gz Zebrafish_3m_COL125_1_2.fq.gz", "fastq fastq", 3535998000.0, 23573320.0, "GSM5400066 r1", "0:150 1:150", "A:1034469165;C:634010669;G:649729630;T:1214431364;N:3357172", 150, 150, null, null, 1034469165, 634010669, 649729630, 1214431364, 3357172, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.34196, null, 0.03294, null, 0.84796, null, 0.53906, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64581, "SRR14915269", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_2_1.fq.gz Zebrafish_3m_COL125_2_2.fq.gz", "fastq fastq", 2034814800.0, 13565432.0, "GSM5400066 r2", "0:150 1:150", "A:561299001;C:400914760;G:406578613;T:664823715;N:1198711", 150, 150, null, null, 561299001, 400914760, 406578613, 664823715, 1198711, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.11368, null, 0.01046, null, 0.93576, null, 0.5358, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64582, "SRR14915270", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_3_1.fq.gz Zebrafish_3m_COL125_3_2.fq.gz", "fastq fastq", 1715258700.0, 11435058.0, "GSM5400066 r3", "0:150 1:150", "A:478425920;C:330213303;G:338928699;T:565440723;N:2250055", 150, 150, null, null, 478425920, 330213303, 338928699, 565440723, 2250055, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13635, null, 0.01121, null, 0.93095, null, 0.51679, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64583, "SRR14915271", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_4_1.fq.gz Zebrafish_3m_COL125_4_2.fq.gz", "fastq fastq", 1715104500.0, 11434030.0, "GSM5400066 r4", "0:150 1:150", "A:484886997;C:327078444;G:334782640;T:566633787;N:1722632", 150, 150, null, null, 484886997, 327078444, 334782640, 566633787, 1722632, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.2998, null, 0.02457, null, 0.88629, null, 0.5217, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64584, "SRR14915272", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_5_2.fq.gz Zebrafish_3m_COL125_5_1.fq.gz", "fastq fastq", 15018441600.0, 100122944.0, "GSM5400066 r5", "0:150 1:150", "A:4129076288;C:3096636754;G:3227410655;T:4544987986;N:20329917", 150, 150, null, null, 4129076288, 3096636754, 3227410655, 4544987986, 20329917, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.39068, null, 0.03076, null, 0.87982, null, 0.53718, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64585, "SRR14915273", "SRX11229458", "SRS9283350", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL125", "GSM5400066", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400066", "GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq", "GSM5400066", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL125_6_2.fq.gz Zebrafish_3m_COL125_6_1.fq.gz", "fastq fastq", 12189015984.0, 140103632.0, "GSM5400066 r6", "0:24 1:150", "A:3884770428;C:2485268235;G:2553035720;T:3242414970;N:23526631", 24, 150, null, null, 3884770428, 2485268235, 2553035720, 3242414970, 23526631, "SRX11229458", "SRS9283350", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35675, null, 0.02764, null, 0.87483, null, 0.54135, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64586, "SRR14915262", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_1_1.fq.gz Zebrafish_3m_COL124_1_2.fq.gz", "fastq fastq", 3548358000.0, 23655720.0, "GSM5400065 r1", "0:150 1:150", "A:1045459196;C:629224836;G:647117553;T:1223292372;N:3264043", 150, 150, null, null, 1045459196, 629224836, 647117553, 1223292372, 3264043, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37097, null, 0.02714, null, 0.83451, null, 0.53691, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64587, "SRR14915263", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_2_1.fq.gz Zebrafish_3m_COL124_2_2.fq.gz", "fastq fastq", 799052400.0, 5327016.0, "GSM5400065 r2", "0:150 1:150", "A:224388479;C:154147586;G:159607563;T:260469676;N:439096", 150, 150, null, null, 224388479, 154147586, 159607563, 260469676, 439096, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.09953, null, 0.00688, null, 0.9361, null, 0.51302, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64588, "SRR14915264", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_3_1.fq.gz Zebrafish_3m_COL124_3_2.fq.gz", "fastq fastq", 1789587900.0, 11930586.0, "GSM5400065 r3", "0:150 1:150", "A:504393249;C:331912683;G:346668689;T:603866933;N:2746346", 150, 150, null, null, 504393249, 331912683, 346668689, 603866933, 2746346, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.16702, null, 0.01095, null, 0.91569, null, 0.53962, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64589, "SRR14915265", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_4_1.fq.gz Zebrafish_3m_COL124_4_2.fq.gz", "fastq fastq", 3069140100.0, 20460934.0, "GSM5400065 r4", "0:150 1:150", "A:874150840;C:568413182;G:589948834;T:1033550871;N:3076373", 150, 150, null, null, 874150840, 568413182, 589948834, 1033550871, 3076373, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.31488, null, 0.01869, null, 0.87444, null, 0.52778, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64590, "SRR14915266", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_5_1.fq.gz Zebrafish_3m_COL124_5_2.fq.gz", "fastq fastq", 15500682600.0, 103337884.0, "GSM5400065 r5", "0:150 1:150", "A:4271460153;C:3150814284;G:3316251816;T:4741035876;N:21120471", 150, 150, null, null, 4271460153, 3150814284, 3316251816, 4741035876, 21120471, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42634, null, 0.02596, null, 0.86789, null, 0.53869, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64591, "SRR14915267", "SRX11229457", "SRS9283352", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL124", "GSM5400065", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400065", "GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq", "GSM5400065", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL124_6_1.fq.gz Zebrafish_3m_COL124_6_2.fq.gz", "fastq fastq", 11909725626.0, 136893398.0, "GSM5400065 r6", "0:24 1:150", "A:3806418177;C:2424097718;G:2498410053;T:3158643077;N:22156601", 24, 150, null, null, 3806418177, 2424097718, 2498410053, 3158643077, 22156601, "SRX11229457", "SRS9283352", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.39256, null, 0.0232, null, 0.85965, null, 0.51961, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64592, "SRR14915256", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_1_1.fq.gz Zebrafish_3m_COL123_1_2.fq.gz", "fastq fastq", 3807078600.0, 25380524.0, "GSM5400064 r1", "0:150 1:150", "A:1122709493;C:680521766;G:695286045;T:1305023708;N:3537588", 150, 150, null, null, 1122709493, 680521766, 695286045, 1305023708, 3537588, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35742, null, 0.02244, null, 0.84433, null, 0.53118, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64593, "SRR14915257", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_2_1.fq.gz Zebrafish_3m_COL123_2_2.fq.gz", "fastq fastq", 1538722800.0, 10258152.0, "GSM5400064 r2", "0:150 1:150", "A:429732126;C:296572020;G:302968410;T:508614732;N:835512", 150, 150, null, null, 429732126, 296572020, 302968410, 508614732, 835512, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13077, null, 0.00804, null, 0.92715, null, 0.53507, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64594, "SRR14915258", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_3_1.fq.gz Zebrafish_3m_COL123_3_2.fq.gz", "fastq fastq", 2031065700.0, 13540438.0, "GSM5400064 r3", "0:150 1:150", "A:572071714;C:383932011;G:395219423;T:677149729;N:2692823", 150, 150, null, null, 572071714, 383932011, 395219423, 677149729, 2692823, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14905, null, 0.00852, null, 0.92598, null, 0.53922, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64595, "SRR14915259", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_4_1.fq.gz Zebrafish_3m_COL123_4_2.fq.gz", "fastq fastq", 2227611000.0, 14850740.0, "GSM5400064 r4", "0:150 1:150", "A:634166526;C:418440499;G:429568047;T:743187782;N:2248146", 150, 150, null, null, 634166526, 418440499, 429568047, 743187782, 2248146, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30527, null, 0.01591, null, 0.8873, null, 0.52617, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64596, "SRR14915260", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_5_1.fq.gz Zebrafish_3m_COL123_5_2.fq.gz", "fastq fastq", 17777963700.0, 118519758.0, "GSM5400064 r5", "0:150 1:150", "A:4902414982;C:3638996050;G:3803098479;T:5408950692;N:24503497", 150, 150, null, null, 4902414982, 3638996050, 3803098479, 5408950692, 24503497, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42515, null, 0.0222, null, 0.87592, null, 0.53827, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64597, "SRR14915261", "SRX11229456", "SRS9283349", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL123", "GSM5400064", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400064", "GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq", "GSM5400064", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL123_6_1.fq.gz Zebrafish_3m_COL123_6_2.fq.gz", "fastq fastq", 13923650172.0, 160041956.0, "GSM5400064 r6", "0:24 1:150", "A:4482285138;C:2834136946;G:2900635816;T:3680471572;N:26120700", 24, 150, null, null, 4482285138, 2834136946, 2900635816, 3680471572, 26120700, "SRX11229456", "SRS9283349", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.38266, null, 0.0197, null, 0.87058, null, 0.53906, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64598, "SRR14915250", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_1_1.fq.gz Zebrafish_3m_COL122_1_2.fq.gz", "fastq fastq", 3414690300.0, 22764602.0, "GSM5400063 r1", "0:150 1:150", "A:1009187609;C:606970670;G:622677920;T:1172654856;N:3199245", 150, 150, null, null, 1009187609, 606970670, 622677920, 1172654856, 3199245, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35805, null, 0.02502, null, 0.83887, null, 0.54238, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64599, "SRR14915251", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_2_1.fq.gz Zebrafish_3m_COL122_2_2.fq.gz", "fastq fastq", 888162300.0, 5921082.0, "GSM5400063 r2", "0:150 1:150", "A:249596683;C:168975194;G:173081430;T:296037426;N:471567", 150, 150, null, null, 249596683, 168975194, 173081430, 296037426, 471567, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.12808, null, 0.008, null, 0.92178, null, 0.53589, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64600, "SRR14915252", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_3_1.fq.gz Zebrafish_3m_COL122_3_2.fq.gz", "fastq fastq", 1491263400.0, 9941756.0, "GSM5400063 r3", "0:150 1:150", "A:420845126;C:278401442;G:289440201;T:500463853;N:2112778", 150, 150, null, null, 420845126, 278401442, 289440201, 500463853, 2112778, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15632, null, 0.00956, null, 0.91786, null, 0.53197, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64601, "SRR14915253", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_4_1.fq.gz Zebrafish_3m_COL122_4_2.fq.gz", "fastq fastq", 2082366900.0, 13882446.0, "GSM5400063 r4", "0:150 1:150", "A:594472285;C:387392031;G:401621477;T:696791581;N:2089526", 150, 150, null, null, 594472285, 387392031, 401621477, 696791581, 2089526, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30145, null, 0.01747, null, 0.88207, null, 0.53561, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64602, "SRR14915254", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_5_1.fq.gz Zebrafish_3m_COL122_5_2.fq.gz", "fastq fastq", 14497371300.0, 96649142.0, "GSM5400063 r5", "0:150 1:150", "A:3998637379;C:2959163742;G:3108117704;T:4411762861;N:19689614", 150, 150, null, null, 3998637379, 2959163742, 3108117704, 4411762861, 19689614, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42459, null, 0.02409, null, 0.87008, null, 0.53134, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64603, "SRR14915255", "SRX11229455", "SRS9283347", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL122", "GSM5400063", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400063", "GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq", "GSM5400063", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL122_6_1.fq.gz Zebrafish_3m_COL122_6_2.fq.gz", "fastq fastq", 11540502150.0, 132649450.0, "GSM5400063 r6", "0:24 1:150", "A:3748135259;C:2346355979;G:2377007855;T:3046617467;N:22385590", 24, 150, null, null, 3748135259, 2346355979, 2377007855, 3046617467, 22385590, "SRX11229455", "SRS9283347", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.37926, null, 0.02105, null, 0.86975, null, 0.53683, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64604, "SRR14915244", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_1_1.fq.gz Zebrafish_3m_COL121_1_2.fq.gz", "fastq fastq", 3798457800.0, 25323052.0, "GSM5400062 r1", "0:150 1:150", "A:1123065806;C:677915734;G:690961588;T:1303011711;N:3502961", 150, 150, null, null, 1123065806, 677915734, 690961588, 1303011711, 3502961, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35985, null, 0.02452, null, 0.84601, null, 0.53759, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64605, "SRR14915245", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_2_1.fq.gz Zebrafish_3m_COL121_2_2.fq.gz", "fastq fastq", 2993954100.0, 19959694.0, "GSM5400062 r2", "0:150 1:150", "A:833149249;C:578520714;G:587711772;T:992742693;N:1829672", 150, 150, null, null, 833149249, 578520714, 587711772, 992742693, 1829672, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.12405, null, 0.00737, null, 0.93208, null, 0.53142, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64606, "SRR14915246", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_3_1.fq.gz Zebrafish_3m_COL121_3_2.fq.gz", "fastq fastq", 2620873800.0, 17472492.0, "GSM5400062 r3", "0:150 1:150", "A:736848542;C:496247795;G:509553396;T:874798630;N:3425437", 150, 150, null, null, 736848542, 496247795, 509553396, 874798630, 3425437, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14484, null, 0.00846, null, 0.92831, null, 0.52606, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64607, "SRR14915247", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_4_1.fq.gz Zebrafish_3m_COL121_4_2.fq.gz", "fastq fastq", 2555651700.0, 17037678.0, "GSM5400062 r4", "0:150 1:150", "A:727711730;C:478951316;G:491267495;T:855146936;N:2574223", 150, 150, null, null, 727711730, 478951316, 491267495, 855146936, 2574223, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30958, null, 0.01649, null, 0.88357, null, 0.52721, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64608, "SRR14915248", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_5_1.fq.gz Zebrafish_3m_COL121_5_2.fq.gz", "fastq fastq", 17315830200.0, 115438868.0, "GSM5400062 r5", "0:150 1:150", "A:4788134328;C:3531893705;G:3690873514;T:5281680486;N:23248167", 150, 150, null, null, 4788134328, 3531893705, 3690873514, 5281680486, 23248167, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42806, null, 0.02272, null, 0.87501, null, 0.53086, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64609, "SRR14915249", "SRX11229454", "SRS9283348", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL121", "GSM5400062", null, "source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample5", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400062", "GSM5400062: Microwell seq datasets of Zebrafish 3m COL121; Danio rerio; RNA Seq", "GSM5400062", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL121_6_1.fq.gz Zebrafish_3m_COL121_6_2.fq.gz", "fastq fastq", 13772162466.0, 158300718.0, "GSM5400062 r6", "0:24 1:150", "A:4478695952;C:2796089790;G:2833403819;T:3637424175;N:26548730", 24, 150, null, null, 4478695952, 2796089790, 2833403819, 3637424175, 26548730, "SRX11229454", "SRS9283348", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.38059, null, 0.02023, null, 0.8744, null, 0.53069, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64610, "SRR14915238", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_1_1.fq.gz Zebrafish_3m_COL100_1_2.fq.gz", "fastq fastq", 3556604100.0, 23710694.0, "GSM5400061 r1", "0:150 1:150", "A:1044932436;C:629993331;G:648367513;T:1229951901;N:3358919", 150, 150, null, null, 1044932436, 629993331, 648367513, 1229951901, 3358919, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35033, null, 0.03534, null, 0.8424, null, 0.53998, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64611, "SRR14915239", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_2_1.fq.gz Zebrafish_3m_COL100_2_2.fq.gz", "fastq fastq", 1122303600.0, 7482024.0, "GSM5400061 r2", "0:150 1:150", "A:308124234;C:218935492;G:226647980;T:368078957;N:516937", 150, 150, null, null, 308124234, 218935492, 226647980, 368078957, 516937, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14015, null, 0.01397, null, 0.92267, null, 0.53345, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64612, "SRR14915240", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_3_1.fq.gz Zebrafish_3m_COL100_3_2.fq.gz", "fastq fastq", 1902935700.0, 12686238.0, "GSM5400061 r3", "0:150 1:150", "A:530508090;C:364747141;G:378080360;T:627094829;N:2505280", 150, 150, null, null, 530508090, 364747141, 378080360, 627094829, 2505280, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14591, null, 0.01368, null, 0.92318, null, 0.52764, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64613, "SRR14915241", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_4_1.fq.gz Zebrafish_3m_COL100_4_2.fq.gz", "fastq fastq", 2091708300.0, 13944722.0, "GSM5400061 r4", "0:150 1:150", "A:589907524;C:398292083;G:411644090;T:689771339;N:2093264", 150, 150, null, null, 589907524, 398292083, 411644090, 689771339, 2093264, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30265, null, 0.02569, null, 0.87878, null, 0.52778, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64614, "SRR14915242", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_5_1.fq.gz Zebrafish_3m_COL100_5_2.fq.gz", "fastq fastq", 14470380600.0, 96469204.0, "GSM5400061 r5", "0:150 1:150", "A:3976109984;C:2977338203;G:3128750825;T:4369015303;N:19166285", 150, 150, null, null, 3976109984, 2977338203, 3128750825, 4369015303, 19166285, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.39903, null, 0.03352, null, 0.87123, null, 0.53374, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64615, "SRR14915243", "SRX11229453", "SRS9283344", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL100", "GSM5400061", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400061", "GSM5400061: Microwell seq datasets of Zebrafish 3m COL100; Danio rerio; RNA Seq", "GSM5400061", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL100_6_1.fq.gz Zebrafish_3m_COL100_6_2.fq.gz", "fastq fastq", 11351686920.0, 130479160.0, "GSM5400061 r6", "0:24 1:150", "A:3600461835;C:2329593104;G:2373162480;T:3026672405;N:21797096", 24, 150, null, null, 3600461835, 2329593104, 2373162480, 3026672405, 21797096, "SRX11229453", "SRS9283344", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36395, null, 0.02826, null, 0.86884, null, 0.53508, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64616, "SRR14915232", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_1_1.fq.gz Zebrafish_3m_COL99_1_2.fq.gz", "fastq fastq", 3652426200.0, 24349508.0, "GSM5400060 r1", "0:150 1:150", "A:1071902143;C:646229900;G:663360231;T:1267527170;N:3406756", 150, 150, null, null, 1071902143, 646229900, 663360231, 1267527170, 3406756, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.35429, null, 0.03345, null, 0.84542, null, 0.53835, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64617, "SRR14915233", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_2_1.fq.gz Zebrafish_3m_COL99_2_2.fq.gz", "fastq fastq", 1040238900.0, 6934926.0, "GSM5400060 r2", "0:150 1:150", "A:287803396;C:200974408;G:207142844;T:343833433;N:484819", 150, 150, null, null, 287803396, 200974408, 207142844, 343833433, 484819, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13479, null, 0.01189, null, 0.92464, null, 0.52747, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64618, "SRR14915234", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_3_1.fq.gz Zebrafish_3m_COL99_3_2.fq.gz", "fastq fastq", 1514139000.0, 10094260.0, "GSM5400060 r3", "0:150 1:150", "A:423615755;C:287340013;G:297750654;T:503304191;N:2128387", 150, 150, null, null, 423615755, 287340013, 297750654, 503304191, 2128387, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15124, null, 0.01397, null, 0.92214, null, 0.53123, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64619, "SRR14915235", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_4_1.fq.gz Zebrafish_3m_COL99_4_2.fq.gz", "fastq fastq", 2017819800.0, 13452132.0, "GSM5400060 r4", "0:150 1:150", "A:570590168;C:380859733;G:392854090;T:671513953;N:2001856", 150, 150, null, null, 570590168, 380859733, 392854090, 671513953, 2001856, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.30652, null, 0.02572, null, 0.8826, null, 0.52816, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64620, "SRR14915236", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_5_1.fq.gz Zebrafish_3m_COL99_5_2.fq.gz", "fastq fastq", 15743678700.0, 104957858.0, "GSM5400060 r5", "0:150 1:150", "A:4325924693;C:3223488191;G:3373994459;T:4799448883;N:20822474", 150, 150, null, null, 4325924693, 3223488191, 3373994459, 4799448883, 20822474, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.40211, null, 0.03229, null, 0.87517, null, 0.53001, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64621, "SRR14915237", "SRX11229452", "SRS9283346", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL99", "GSM5400060", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400060", "GSM5400060: Microwell seq datasets of Zebrafish 3m COL99; Danio rerio; RNA Seq", "GSM5400060", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL99_6_1.fq.gz Zebrafish_3m_COL99_6_2.fq.gz", "fastq fastq", 12429027060.0, 142862380.0, "GSM5400060 r6", "0:24 1:150", "A:3951522730;C:2536070687;G:2600383059;T:3317626484;N:23424100", 24, 150, null, null, 3951522730, 2536070687, 2600383059, 3317626484, 23424100, "SRX11229452", "SRS9283346", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36917, null, 0.02821, null, 0.87004, null, 0.53364, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64622, "SRR14915226", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_1_1.fq.gz Zebrafish_3m_COL98_1_2.fq.gz", "fastq fastq", 3624714000.0, 24164760.0, "GSM5400059 r1", "0:150 1:150", "A:1066553242;C:642905490;G:659704162;T:1252114639;N:3436467", 150, 150, null, null, 1066553242, 642905490, 659704162, 1252114639, 3436467, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.34741, null, 0.03528, null, 0.84453, null, 0.53546, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64623, "SRR14915227", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_2_1.fq.gz Zebrafish_3m_COL98_2_2.fq.gz", "fastq fastq", 173439300.0, 1156262.0, "GSM5400059 r2", "0:150 1:150", "A:47342402;C:33935120;G:35092394;T:56977054;N:92330", 150, 150, null, null, 47342402, 33935120, 35092394, 56977054, 92330, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.12545, null, 0.01098, null, 0.93243, null, 0.54306, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64624, "SRR14915228", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_3_1.fq.gz Zebrafish_3m_COL98_3_2.fq.gz", "fastq fastq", 808542300.0, 5390282.0, "GSM5400059 r3", "0:150 1:150", "A:225940008;C:154071800;G:159993148;T:267245702;N:1291642", 150, 150, null, null, 225940008, 154071800, 159993148, 267245702, 1291642, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.15957, null, 0.01505, null, 0.91875, null, 0.52285, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64625, "SRR14915229", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_4_1.fq.gz Zebrafish_3m_COL98_4_2.fq.gz", "fastq fastq", 1850343600.0, 12335624.0, "GSM5400059 r4", "0:150 1:150", "A:526260511;C:350787029;G:360347928;T:611111854;N:1836278", 150, 150, null, null, 526260511, 350787029, 360347928, 611111854, 1836278, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.29613, null, 0.02562, null, 0.88284, null, 0.52988, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64626, "SRR14915230", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_5_1.fq.gz Zebrafish_3m_COL98_5_2.fq.gz", "fastq fastq", 15707112300.0, 104714082.0, "GSM5400059 r5", "0:150 1:150", "A:4304304502;C:3249843343;G:3418070484;T:4713467133;N:21426838", 150, 150, null, null, 4304304502, 3249843343, 3418070484, 4713467133, 21426838, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.39286, null, 0.03318, null, 0.87756, null, 0.54516, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64627, "SRR14915231", "SRX11229451", "SRS9283345", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL98", "GSM5400059", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400059", "GSM5400059: Microwell seq datasets of Zebrafish 3m COL98; Danio rerio; RNA Seq", "GSM5400059", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL98_6_1.fq.gz Zebrafish_3m_COL98_6_2.fq.gz", "fastq fastq", 12478600356.0, 143432188.0, "GSM5400059 r6", "0:24 1:150", "A:3932781792;C:2576294604;G:2611240487;T:3334472497;N:23810976", 24, 150, null, null, 3932781792, 2576294604, 2611240487, 3334472497, 23810976, "SRX11229451", "SRS9283345", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36157, null, 0.02897, null, 0.8687, null, 0.53759, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64628, "SRR14915224", "SRX11229450", "SRS9283342", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL97", "GSM5400058", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400058", "GSM5400058: Microwell seq datasets of Zebrafish 3m COL97; Danio rerio; RNA Seq", "GSM5400058", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL97_5_1.fq.gz Zebrafish_3m_COL97_5_2.fq.gz", "fastq fastq", 927595500.0, 6183970.0, "GSM5400058 r1", "0:150 1:150", "A:255884199;C:188560785;G:198076220;T:283826691;N:1247605", 150, 150, null, null, 255884199, 188560785, 198076220, 283826691, 1247605, "SRX11229450", "SRS9283342", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.42086, null, 0.02942, null, 0.87696, null, 0.54381, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64629, "SRR14915225", "SRX11229450", "SRS9283342", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL97", "GSM5400058", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400058", "GSM5400058: Microwell seq datasets of Zebrafish 3m COL97; Danio rerio; RNA Seq", "GSM5400058", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL97_6_1.fq.gz Zebrafish_3m_COL97_6_2.fq.gz", "fastq fastq", 14001509082.0, 160936886.0, "GSM5400058 r2", "0:24 1:150", "A:4701235778;C:2740737235;G:2786528848;T:3746127683;N:26879538", 24, 150, null, null, 4701235778, 2740737235, 2786528848, 3746127683, 26879538, "SRX11229450", "SRS9283342", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36239, null, 0.02536, null, 0.87576, null, 0.54101, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64630, "SRR14915218", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_1_1.fq.gz Zebrafish_3m_COL96_1_2.fq.gz", "fastq fastq", 3891051900.0, 25940346.0, "GSM5400057 r1", "0:150 1:150", "A:1142990535;C:685116335;G:704775786;T:1354535138;N:3634106", 150, 150, null, null, 1142990535, 685116335, 704775786, 1354535138, 3634106, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36269, null, 0.03437, null, 0.8407, null, 0.53551, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64631, "SRR14915219", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_2_1.fq.gz Zebrafish_3m_COL96_2_2.fq.gz", "fastq fastq", 1992177000.0, 13281180.0, "GSM5400057 r2", "0:150 1:150", "A:551582385;C:382459359;G:391655782;T:665311725;N:1167749", 150, 150, null, null, 551582385, 382459359, 391655782, 665311725, 1167749, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.12183, null, 0.01058, null, 0.93016, null, 0.52788, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64632, "SRR14915220", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_3_1.fq.gz Zebrafish_3m_COL96_3_2.fq.gz", "fastq fastq", 1805537100.0, 12036914.0, "GSM5400057 r3", "0:150 1:150", "A:504443194;C:340650452;G:351827682;T:606194855;N:2420917", 150, 150, null, null, 504443194, 340650452, 351827682, 606194855, 2420917, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.14371, null, 0.01233, null, 0.9276, null, 0.536, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64633, "SRR14915221", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_4_1.fq.gz Zebrafish_3m_COL96_4_2.fq.gz", "fastq fastq", 1828148100.0, 12187654.0, "GSM5400057 r4", "0:150 1:150", "A:517986030;C:341911005;G:352442273;T:613950583;N:1858209", 150, 150, null, null, 517986030, 341911005, 352442273, 613950583, 1858209, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.31276, null, 0.02461, null, 0.88304, null, 0.52934, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64634, "SRR14915222", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_5_2.fq.gz Zebrafish_3m_COL96_5_1.fq.gz", "fastq fastq", 16188716100.0, 107924774.0, "GSM5400057 r5", "0:150 1:150", "A:4443625890;C:3304209394;G:3465199255;T:4954295691;N:21385870", 150, 150, null, null, 4443625890, 3304209394, 3465199255, 4954295691, 21385870, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.41682, null, 0.03178, null, 0.86927, null, 0.53589, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64635, "SRR14915223", "SRX11229449", "SRS9283343", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL96", "GSM5400057", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400057", "GSM5400057: Microwell seq datasets of Zebrafish 3m COL96; Danio rerio; RNA Seq", "GSM5400057", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL96_6_2.fq.gz Zebrafish_3m_COL96_6_1.fq.gz", "fastq fastq", 13135314636.0, 150980628.0, "GSM5400057 r6", "0:24 1:150", "A:4168403321;C:2671620743;G:2751967185;T:3518630376;N:24693011", 24, 150, null, null, 4168403321, 2671620743, 2751967185, 3518630376, 24693011, "SRX11229449", "SRS9283343", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.38174, null, 0.02813, null, 0.86701, null, 0.5388, null, 24, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64636, "SRR14915212", "SRX11229448", "SRS9283340", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL95", "GSM5400056", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400056", "GSM5400056: Microwell seq datasets of Zebrafish 3m COL95; Danio rerio; RNA Seq", "GSM5400056", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL95_1_1.fq.gz Zebrafish_3m_COL95_1_2.fq.gz", "fastq fastq", 4236926100.0, 28246174.0, "GSM5400056 r1", "0:150 1:150", "A:1245306187;C:746214572;G:767187091;T:1474251499;N:3966751", 150, 150, null, null, 1245306187, 746214572, 767187091, 1474251499, 3966751, "SRX11229448", "SRS9283340", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.36054, null, 0.03582, null, 0.83984, null, 0.51062, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [64637, "SRR14915213", "SRX11229448", "SRS9283340", "SRP324000", "PRJNA737474", "Construction the larval and adult zebrafish cell atlas at single cell resolution", "GSE178150", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies  we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However  systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here  we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols  which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila  and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf  3 replicates  10 fish for each replicate and adult 90 day  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA737471", "pubmed:36229673", null, "Microwell seq datasets of Zebrafish 3m COL95", "GSM5400056", null, "source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism", "Microwell seq datasets of Zebrafish 3m 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 5 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 6 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. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 3m sample6", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:3 month 90 day|tissue:whole organism", "GSM5400056", "GSM5400056: Microwell seq datasets of Zebrafish 3m COL95; Danio rerio; RNA Seq", "GSM5400056", null, "1", "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP324000", null, null, "Zebrafish_3m_COL95_2_1.fq.gz Zebrafish_3m_COL95_2_2.fq.gz", "fastq fastq", 1264441200.0, 8429608.0, "GSM5400056 r2", "0:150 1:150", "A:350425519;C:241301219;G:249817297;T:422260496;N:636669", 150, 150, null, null, 350425519, 241301219, 249817297, 422260496, 636669, "SRX11229448", "SRS9283340", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 1, 0.13634, null, 0.01229, null, 0.92401, null, 0.53784, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-06-25", "Adult", "Adult", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 711, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"technology\" = :p1 order by rowid limit 101", "params": {"p0": "Adult", "p1": "microwellseq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "cDNA", "label": "cDNA", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 424, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 287, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "DNBSEQ", "label": "DNBSEQ", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&experiment.platform=DNBSEQ", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "Adult", "label": "Adult", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=microwellseq", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "Adult", "label": "Adult", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&tissue_curation=Whole+Organism", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq", "results": [{"value": "microwellseq", "label": "microwellseq", "count": 711, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": "64637", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Adult&technology=microwellseq&_next=64637", "private": false, "allow_execute_sql": true, "query_ms": 64.75006400069105}