{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and technology = \"microwellseq\"", "rows": [[52169, "SRR10902878", "SRX7571048", "SRS6006649", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "72hpf 2", "GSM4274624", null, "source name:embryo|strain:Tubingen|tissue:embryo|genotype:wild type", "72hpf 2", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "embryo", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:embryo|genotype:wild type", "GSM4274624", "GSM4274624: 72hpf 2; Danio rerio; RNA Seq", "GSM4274624", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274624", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "72hpf2.bam", "bam", 44540357958.0, 147484629.0, "GSM4274624 r1", "0:151 1:151", "A:11658483828;C:7854882099;G:7912135327;T:17103979590;N:10877114", 151, 151, null, null, 11658483828, 7854882099, 7912135327, 17103979590, 10877114, "SRX7571048", "SRS6006649", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.70491, 0.0, 0.03368, 1.0, 0.81903, null, 0.50131, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [52170, "SRR10902877", "SRX7571047", "SRS6006648", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "72hpf 1", "GSM4274623", null, "source name:embryo|strain:Tubingen|tissue:embryo|genotype:wild type", "72hpf 1", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "embryo", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:embryo|genotype:wild type", "GSM4274623", "GSM4274623: 72hpf 1; Danio rerio; RNA Seq", "GSM4274623", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274623", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "72hpf1.bam", "bam", 10980000636.0, 36357618.0, "GSM4274623 r1", "0:151 1:151", "A:2869082796;C:1850640633;G:1873838761;T:4383874336;N:2564110", 151, 151, null, null, 2869082796, 1850640633, 1873838761, 4383874336, 2564110, "SRX7571047", "SRS6006648", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.7282, 0.0, 0.02753, 1.0, 0.81716, null, 0.47137, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [64515, "SRR17137061", "SRX13321491", "SRS11229252", "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 72hpf COL103", "GSM5718327", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf COL103", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718327", "GSM5718327: Microwell seq datasets of Zebrafish 72hpf COL103; Danio rerio; RNA Seq", "GSM5718327", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL103.bam", "bam", 97437769842.0, 559987183.0, "GSM5718327 r1", "0:24 1:150", "A:28425257606;C:21026057575;G:22210354179;T:25724166722;N:51933760", 24, 150, null, null, 28425257606, 21026057575, 22210354179, 25724166722, 51933760, "SRX13321491", "SRS11229252", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00232, 0.76296, 0.00214, 0.09247, 0.99975, 0.7963, 0.58333, 0.50975, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64516, "SRR17137060", "SRX13321490", "SRS11229251", "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 72hpf COL102", "GSM5718326", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf COL102", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718326", "GSM5718326: Microwell seq datasets of Zebrafish 72hpf COL102; Danio rerio; RNA Seq", "GSM5718326", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL102.bam", "bam", 99647119878.0, 572684597.0, "GSM5718326 r1", "0:24 1:150", "A:29163675513;C:21410312143;G:22841561495;T:26179135838;N:52434889", 24, 150, null, null, 29163675513, 21410312143, 22841561495, 26179135838, 52434889, "SRX13321490", "SRS11229251", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00211, 0.75462, 0.00197, 0.08783, 0.99979, 0.79614, 0.6, 0.48777, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64517, "SRR17137059", "SRX13321489", "SRS11229250", "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 72hpf COL101", "GSM5718325", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf COL101", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718325", "GSM5718325: Microwell seq datasets of Zebrafish 72hpf COL101; Danio rerio; RNA Seq", "GSM5718325", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL101.bam", "bam", 103850532360.0, 596842140.0, "GSM5718325 r1", "0:24 1:150", "A:30253504994;C:22208170461;G:23486370057;T:27846281411;N:56205437", 24, 150, null, null, 30253504994, 22208170461, 23486370057, 27846281411, 56205437, "SRX13321489", "SRS11229250", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00248, 0.76955, 0.00238, 0.09242, 0.99985, 0.78549, 0.0, 0.48332, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64518, "SRR17137058", "SRX13321488", "SRS11229249", "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 72hpf COL100", "GSM5718324", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718324", "GSM5718324: Microwell seq datasets of Zebrafish 72hpf COL100; Danio rerio; RNA Seq", "GSM5718324", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL100.bam", "bam", 79732033224.0, 458230076.0, "GSM5718324 r1", "0:24 1:150", "A:23142121477;C:17273443279;G:18152994838;T:21124595570;N:38878060", 24, 150, null, null, 23142121477, 17273443279, 18152994838, 21124595570, 38878060, "SRX13321488", "SRS11229249", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.0019, 0.78954, 0.00176, 0.1, 0.99977, 0.79302, 0.45454, 0.53183, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64519, "SRR17137057", "SRX13321487", "SRS11229248", "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 72hpf COL99", "GSM5718323", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718323", "GSM5718323: Microwell seq datasets of Zebrafish 72hpf COL99; Danio rerio; RNA Seq", "GSM5718323", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL99.bam", "bam", 57905355774.0, 332789401.0, "GSM5718323 r1", "0:24 1:150", "A:16732054497;C:12484254815;G:13099812159;T:15561038953;N:28195350", 24, 150, null, null, 16732054497, 12484254815, 13099812159, 15561038953, 28195350, "SRX13321487", "SRS11229248", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.0023, 0.79516, 0.00213, 0.10777, 0.99977, 0.79413, 0.5, 0.52425, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64520, "SRR17137056", "SRX13321486", "SRS11229247", "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 72hpf COL98", "GSM5718322", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718322", "GSM5718322: Microwell seq datasets of Zebrafish 72hpf COL98; Danio rerio; RNA Seq", "GSM5718322", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL98.bam", "bam", 133922399388.0, 769668962.0, "GSM5718322 r1", "0:24 1:150", "A:39157671234;C:28685783001;G:30222645162;T:35787052837;N:69247154", 24, 150, null, null, 39157671234, 28685783001, 30222645162, 35787052837, 69247154, "SRX13321486", "SRS11229247", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00205, 0.77779, 0.00189, 0.10045, 0.99977, 0.7903, 0.36363, 0.52076, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64521, "SRR17137055", "SRX13321485", "SRS11229246", "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 72hpf COL97", "GSM5718321", null, "source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism", "Microwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample3", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5718321", "GSM5718321: Microwell seq datasets of Zebrafish 72hpf COL97; Danio rerio; RNA Seq", "GSM5718321", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL97.bam", "bam", 102882979782.0, 591281493.0, "GSM5718321 r1", "0:24 1:150", "A:30066107926;C:21991309044;G:23041144876;T:27728508333;N:55909603", 24, 150, null, null, 30066107926, 21991309044, 23041144876, 27728508333, 55909603, "SRX13321485", "SRS11229246", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00231, 0.78387, 0.00216, 0.09479, 0.99977, 0.78638, 0.63636, 0.48401, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-12-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64522, "SRR17075126", "SRX13263481", "SRS11185248", "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, "Micorwell seq datasets of Zebrafish 72hpf COL92", "GSM5709061", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL92", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709061", "GSM5709061: Micorwell seq datasets of Zebrafish 72hpf COL92; Danio rerio; RNA Seq", "GSM5709061", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL92.bam", "bam", 93305697882.0, 536239643.0, "GSM5709061 r1", "0:24 1:150", "A:27107741517;C:19830183542;G:20994123402;T:25327971257;N:45678164", 24, 150, null, null, 27107741517, 19830183542, 20994123402, 25327971257, 45678164, "SRX13263481", "SRS11185248", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00194, 0.78236, 0.00179, 0.10164, 0.99975, 0.78618, 0.75, 0.48898, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64523, "SRR17075125", "SRX13263480", "SRS11185247", "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, "Micorwell seq datasets of Zebrafish 72hpf COL91", "GSM5709060", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL91", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709060", "GSM5709060: Micorwell seq datasets of Zebrafish 72hpf COL91; Danio rerio; RNA Seq", "GSM5709060", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL91.bam", "bam", 96227810904.0, 553033396.0, "GSM5709060 r1", "0:24 1:150", "A:27923073482;C:20564137902;G:21719882675;T:25970776374;N:49940471", 24, 150, null, null, 27923073482, 20564137902, 21719882675, 25970776374, 49940471, "SRX13263480", "SRS11185247", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.0019, 0.78115, 0.00184, 0.10758, 0.99989, 0.78725, 0.4, 0.49305, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64524, "SRR17075124", "SRX13263479", "SRS11185246", "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, "Micorwell seq datasets of Zebrafish 72hpf COL90", "GSM5709059", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL90", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709059", "GSM5709059: Micorwell seq datasets of Zebrafish 72hpf COL90; Danio rerio; RNA Seq", "GSM5709059", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL90.bam", "bam", 101004540858.0, 580485867.0, "GSM5709059 r1", "0:24 1:150", "A:29424345909;C:21610893920;G:22734702528;T:27180463498;N:54135003", 24, 150, null, null, 29424345909, 21610893920, 22734702528, 27180463498, 54135003, "SRX13263479", "SRS11185246", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00188, 0.78353, 0.00176, 0.10575, 0.99981, 0.78699, 0.55555, 0.50829, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64525, "SRR17075123", "SRX13263478", "SRS11185245", "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, "Micorwell seq datasets of Zebrafish 72hpf COL89", "GSM5709058", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL89", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709058", "GSM5709058: Micorwell seq datasets of Zebrafish 72hpf COL89; Danio rerio; RNA Seq", "GSM5709058", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL89.bam", "bam", 103228879080.0, 593269420.0, "GSM5709058 r1", "0:24 1:150", "A:30122538038;C:21933106979;G:23172314020;T:27949125385;N:51794658", 24, 150, null, null, 30122538038, 21933106979, 23172314020, 27949125385, 51794658, "SRX13263478", "SRS11185245", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00229, 0.78058, 0.00208, 0.11813, 0.99967, 0.78642, 0.4375, 0.51666, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64526, "SRR17075130", "SRX13263477", "SRS11185244", "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, "Micorwell seq datasets of Zebrafish 72hpf COL96", "GSM5709065", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709065", "GSM5709065: Micorwell seq datasets of Zebrafish 72hpf COL96; Danio rerio; RNA Seq", "GSM5709065", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL96.bam", "bam", 72161390838.0, 414720637.0, "GSM5709065 r1", "0:24 1:150", "A:20858972054;C:15631755598;G:16378791674;T:19256108785;N:35762727", 24, 150, null, null, 20858972054, 15631755598, 16378791674, 19256108785, 35762727, "SRX13263477", "SRS11185244", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.0024, 0.78585, 0.00221, 0.10389, 0.99971, 0.79099, 0.64285, 0.51929, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64527, "SRR17075129", "SRX13263476", "SRS11185243", "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, "Micorwell seq datasets of Zebrafish 72hpf COL95", "GSM5709064", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709064", "GSM5709064: Micorwell seq datasets of Zebrafish 72hpf COL95; Danio rerio; RNA Seq", "GSM5709064", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL95.bam", "bam", 116725350900.0, 670835350.0, "GSM5709064 r1", "0:24 1:150", "A:33766055210;C:25258192198;G:26422558801;T:31219012086;N:59532605", 24, 150, null, null, 33766055210, 25258192198, 26422558801, 31219012086, 59532605, "SRX13263476", "SRS11185243", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00223, 0.78242, 0.00205, 0.10222, 0.99973, 0.7948, 0.76923, 0.51107, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64528, "SRR17075128", "SRX13263475", "SRS11185241", "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, "Micorwell seq datasets of Zebrafish 72hpf COL94", "GSM5709063", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL94", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709063", "GSM5709063: Micorwell seq datasets of Zebrafish 72hpf COL94; Danio rerio; RNA Seq", "GSM5709063", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL94.bam", "bam", 115204393758.0, 662094217.0, "GSM5709063 r1", "0:24 1:150", "A:33385976074;C:24728619684;G:25999313932;T:31027995525;N:62488543", 24, 150, null, null, 33385976074, 24728619684, 25999313932, 31027995525, 62488543, "SRX13263475", "SRS11185241", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00227, 0.78471, 0.00206, 0.10458, 0.99967, 0.78591, 0.4375, 0.50275, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64529, "SRR17075127", "SRX13263474", "SRS11185242", "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, "Micorwell seq datasets of Zebrafish 72hpf COL93", "GSM5709062", null, "source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL93", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample2", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5709062", "GSM5709062: Micorwell seq datasets of Zebrafish 72hpf COL93; Danio rerio; RNA Seq", "GSM5709062", 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, "assembly:GRCz11|intentional duplicate", "Zebrafish_72hpf_COL93.bam", "bam", 109890007632.0, 631551768.0, "GSM5709062 r1", "0:24 1:150", "A:31784495967;C:23590735781;G:24835459995;T:29625393694;N:53922195", 24, 150, null, null, 31784495967, 23590735781, 24835459995, 29625393694, 53922195, "SRX13263474", "SRS11185242", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00221, 0.77545, 0.002, 0.11238, 0.99969, 0.78879, 0.4375, 0.50979, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64530, "SRR17010806", "SRX13200959", "SRS11127611", "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, "Micorwell seq datasets of Zebrafish 72hpf COL88", "GSM5699934", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL88", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699934", "GSM5699934: Micorwell seq datasets of Zebrafish 72hpf COL88; Danio rerio; RNA Seq", "GSM5699934", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL88.bam", "bam", 105325546890.0, 605319235.0, "GSM5699934 r1", "0:24 1:150", "A:30618141170;C:22639431941;G:23832910711;T:28175599693;N:59463375", 24, 150, null, null, 30618141170, 22639431941, 23832910711, 28175599693, 59463375, "SRX13200959", "SRS11127611", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00204, 0.77653, 0.00184, 0.1038, 0.99969, 0.78896, 0.4, 0.49664, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64531, "SRR17010805", "SRX13200958", "SRS11127610", "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, "Micorwell seq datasets of Zebrafish 72hpf COL87", "GSM5699933", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL87", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699933", "GSM5699933: Micorwell seq datasets of Zebrafish 72hpf COL87; Danio rerio; RNA Seq", "GSM5699933", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL87.bam", "bam", 104410657848.0, 600061252.0, "GSM5699933 r1", "0:24 1:150", "A:30448105235;C:22372529466;G:23651054417;T:27884763811;N:54204919", 24, 150, null, null, 30448105235, 22372529466, 23651054417, 27884763811, 54204919, "SRX13200958", "SRS11127610", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00239, 0.76912, 0.00221, 0.11084, 0.99971, 0.78847, 0.5, 0.51741, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64532, "SRR17010804", "SRX13200957", "SRS11127609", "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, "Micorwell seq datasets of Zebrafish 72hpf COL86", "GSM5699932", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL86", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699932", "GSM5699932: Micorwell seq datasets of Zebrafish 72hpf COL86; Danio rerio; RNA Seq", "GSM5699932", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL86.bam", "bam", 85539017526.0, 491603549.0, "GSM5699932 r1", "0:24 1:150", "A:24891444353;C:18382714837;G:19465935988;T:22755762595;N:43159753", 24, 150, null, null, 24891444353, 18382714837, 19465935988, 22755762595, 43159753, "SRX13200957", "SRS11127609", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00186, 0.7737, 0.00168, 0.10503, 0.99973, 0.78553, 0.35714, 0.52806, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64533, "SRR17010803", "SRX13200956", "SRS11127608", "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, "Micorwell seq datasets of Zebrafish 72hpf COL85", "GSM5699931", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL85", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699931", "GSM5699931: Micorwell seq datasets of Zebrafish 72hpf COL85; Danio rerio; RNA Seq", "GSM5699931", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL85.bam", "bam", 96579499182.0, 555054593.0, "GSM5699931 r1", "0:24 1:150", "A:28258999810;C:20566647022;G:21776511096;T:25928948228;N:48393026", 24, 150, null, null, 28258999810, 20566647022, 21776511096, 25928948228, 48393026, "SRX13200956", "SRS11127608", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00215, 0.77075, 0.00203, 0.09684, 0.99981, 0.78348, 0.44444, 0.50291, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64534, "SRR17010802", "SRX13200955", "SRS11127607", "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, "Micorwell seq datasets of Zebrafish 72hpf COL84", "GSM5699930", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL84", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699930", "GSM5699930: Micorwell seq datasets of Zebrafish 72hpf COL84; Danio rerio; RNA Seq", "GSM5699930", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL84.bam", "bam", 95402087292.0, 548287858.0, "GSM5699930 r1", "0:24 1:150", "A:27920812951;C:20371734068;G:21595614980;T:25463535654;N:50389639", 24, 150, null, null, 27920812951, 20371734068, 21595614980, 25463535654, 50389639, "SRX13200955", "SRS11127607", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00199, 0.76291, 0.00186, 0.09597, 0.99981, 0.79001, 0.3, 0.50069, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64535, "SRR17010801", "SRX13200954", "SRS11127606", "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, "Micorwell seq datasets of Zebrafish 72hpf COL83", "GSM5699929", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL83", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699929", "GSM5699929: Micorwell seq datasets of Zebrafish 72hpf COL83; Danio rerio; RNA Seq", "GSM5699929", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL83.bam", "bam", 94589605254.0, 543618421.0, "GSM5699929 r1", "0:24 1:150", "A:27596905697;C:20243328527;G:21378738112;T:25321573995;N:49058923", 24, 150, null, null, 27596905697, 20243328527, 21378738112, 25321573995, 49058923, "SRX13200954", "SRS11127606", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00216, 0.77625, 0.00202, 0.09982, 0.99979, 0.78831, 0.36363, 0.51012, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64536, "SRR17010800", "SRX13200953", "SRS11127605", "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, "Micorwell seq datasets of Zebrafish 72hpf COL82", "GSM5699928", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL82", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699928", "GSM5699928: Micorwell seq datasets of Zebrafish 72hpf COL82; Danio rerio; RNA Seq", "GSM5699928", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL82.bam", "bam", 89062661598.0, 511854377.0, "GSM5699928 r1", "0:24 1:150", "A:26102790989;C:19094974289;G:20282271482;T:23541508213;N:41116625", 24, 150, null, null, 26102790989, 19094974289, 20282271482, 23541508213, 41116625, "SRX13200953", "SRS11127605", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00227, 0.76728, 0.00206, 0.10248, 0.99969, 0.79196, 0.29411, 0.53203, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [64537, "SRR17010799", "SRX13200952", "SRS11127604", "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, "Micorwell seq datasets of Zebrafish 72hpf COL81", "GSM5699927", null, "source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism", "Micorwell seq datasets of Zebrafish 72hpf COL81", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 72hpf sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:72 hours|tissue:whole organism", "GSM5699927", "GSM5699927: Micorwell seq datasets of Zebrafish 72hpf COL81; Danio rerio; RNA Seq", "GSM5699927", 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, "assembly:Danio rerio reference genome GRCz11|intentional duplicate", "Zebrafish_72hpf_COL81.bam", "bam", 97306386444.0, 559232106.0, "GSM5699927 r1", "0:24 1:150", "A:28504741466;C:20782464199;G:21987624297;T:25985173510;N:46382972", 24, 150, null, null, 28504741466, 20782464199, 21987624297, 25985173510, 46382972, "SRX13200952", "SRS11127604", "SRA1244752", "GEO", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00232, 0.76473, 0.00224, 0.09727, 0.99987, 0.79153, 0.66666, 0.51198, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2021-11-22", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69030, "SRR18915947", "SRX14993869", "SRS12743202", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL81", "GSM6065257", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL81", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065257", "GSM6065257: Micorwell seq datasets of Zebrafish 21d COL81; Danio rerio; RNA Seq", "GSM6065257 r1", "GSM6065257", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL81.bam", "bam", 85166719644.0, 489463906.0, "GSM6065257 r1", "0:24 1:150", "A:25394489421;C:18330098932;G:19514700318;T:21879684357;N:47746616", 24, 150, null, null, 25394489421, 18330098932, 19514700318, 21879684357, 47746616, "SRX14993869", "SRS12743202", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00199, 0.71127, 0.00178, 0.07816, 0.99967, 0.81982, 0.52941, 0.5245, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69031, "SRR18915948", "SRX14993868", "SRS12743201", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL80", "GSM6065256", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL80", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065256", "GSM6065256: Micorwell seq datasets of Zebrafish 21d COL80; Danio rerio; RNA Seq", "GSM6065256 r1", "GSM6065256", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL80.bam", "bam", 111497237106.0, 640788719.0, "GSM6065256 r1", "0:24 1:150", "A:32950253336;C:24245222125;G:25622395050;T:28613565536;N:65801059", 24, 150, null, null, 32950253336, 24245222125, 25622395050, 28613565536, 65801059, "SRX14993868", "SRS12743201", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00189, 0.72353, 0.00175, 0.08106, 0.99977, 0.81655, 0.81818, 0.53595, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69033, "SRR18915950", "SRX14993866", "SRS12743199", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL78", "GSM6065254", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL78", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065254", "GSM6065254: Micorwell seq datasets of Zebrafish 21d COL78; Danio rerio; RNA Seq", "GSM6065254 r1", "GSM6065254", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL78.bam", "bam", 127934220708.0, 735254142.0, "GSM6065254 r1", "0:24 1:150", "A:38850692930;C:27416030835;G:29159416091;T:32431776464;N:76304388", 24, 150, null, null, 38850692930, 27416030835, 29159416091, 32431776464, 76304388, "SRX14993866", "SRS12743199", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00186, 0.68867, 0.0017, 0.07269, 0.99975, 0.82373, 0.58333, 0.55189, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69034, "SRR18915951", "SRX14993865", "SRS12743198", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL77", "GSM6065253", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL77", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065253", "GSM6065253: Micorwell seq datasets of Zebrafish 21d COL77; Danio rerio; RNA Seq", "GSM6065253 r1", "GSM6065253", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL77.bam", "bam", 80820134394.0, 464483531.0, "GSM6065253 r1", "0:24 1:150", "A:24296572822;C:17324334100;G:18535708700;T:20617475238;N:46043534", 24, 150, null, null, 24296572822, 17324334100, 18535708700, 20617475238, 46043534, "SRX14993865", "SRS12743198", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00221, 0.70755, 0.00209, 0.07288, 0.99981, 0.81164, 0.55555, 0.556, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69036, "SRR18915953", "SRX14993863", "SRS12743196", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL75", "GSM6065251", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL75", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065251", "GSM6065251: Micorwell seq datasets of Zebrafish 21d COL75; Danio rerio; RNA Seq", "GSM6065251 r1", "GSM6065251", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL75.bam", "bam", 98096443014.0, 563772661.0, "GSM6065251 r1", "0:24 1:150", "A:29548798624;C:21201260754;G:22624551512;T:24659959036;N:61873088", 24, 150, null, null, 29548798624, 21201260754, 22624551512, 24659959036, 61873088, "SRX14993863", "SRS12743196", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.0022, 0.68029, 0.00201, 0.07741, 0.99971, 0.82477, 0.42857, 0.55407, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69037, "SRR18915954", "SRX14993862", "SRS12743195", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL74", "GSM6065250", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL74", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6065250", "GSM6065250: Micorwell seq datasets of Zebrafish 21d COL74; Danio rerio; RNA Seq", "GSM6065250 r1", "GSM6065250", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL74.bam", "bam", 90212334408.0, 518461692.0, "GSM6065250 r1", "0:24 1:150", "A:27133186645;C:19479937195;G:20822007282;T:22722889235;N:54314051", 24, 150, null, null, 27133186645, 19479937195, 20822007282, 22722889235, 54314051, "SRX14993862", "SRS12743195", "SRA1409755", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00205, 0.67703, 0.00193, 0.07756, 0.99979, 0.82745, 0.4, 0.54974, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-25", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69039, "SRR18642996", "SRX14746258", "SRS12507766", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL72", "GSM6019657", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL72", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019657", "GSM6019657: Micorwell seq datasets of Zebrafish 21d COL72; Danio rerio; RNA Seq", "GSM6019657 r1", "GSM6019657", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL72.bam", "bam", 105217499154.0, 604698271.0, "GSM6019657 r1", "0:24 1:150", "A:32147374909;C:22510722936;G:23860762626;T:26641243924;N:57394759", 24, 150, null, null, 32147374909, 22510722936, 23860762626, 26641243924, 57394759, "SRX14746258", "SRS12507766", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00186, 0.68944, 0.00174, 0.07203, 0.99979, 0.82191, 0.4, 0.56516, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69041, "SRR18642998", "SRX14746256", "SRS12507762", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL70", "GSM6019655", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL70", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019655", "GSM6019655: Micorwell seq datasets of Zebrafish 21d COL70; Danio rerio; RNA Seq", "GSM6019655 r1", "GSM6019655", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL70.bam", "bam", 116138687280.0, 667463720.0, "GSM6019655 r1", "0:24 1:150", "A:35176309010;C:24925275975;G:26453654207;T:29505834294;N:77613794", 24, 150, null, null, 35176309010, 24925275975, 26453654207, 29505834294, 77613794, "SRX14746256", "SRS12507762", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00165, 0.68567, 0.00151, 0.08303, 0.99977, 0.81442, 0.36363, 0.55872, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69042, "SRR18642999", "SRX14746255", "SRS12507763", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL69", "GSM6019654", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL69", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019654", "GSM6019654: Micorwell seq datasets of Zebrafish 21d COL69; Danio rerio; RNA Seq", "GSM6019654 r1", "GSM6019654", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL69.bam", "bam", 115431686130.0, 663400495.0, "GSM6019654 r1", "0:24 1:150", "A:35119787654;C:24596504518;G:26309960633;T:29342805291;N:62628034", 24, 150, null, null, 35119787654, 24596504518, 26309960633, 29342805291, 62628034, "SRX14746255", "SRS12507763", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00227, 0.67115, 0.00209, 0.08394, 0.99969, 0.81884, 0.46666, 0.54042, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69043, "SRR18643000", "SRX14746254", "SRS12507761", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL68", "GSM6019653", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL68", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019653", "GSM6019653: Micorwell seq datasets of Zebrafish 21d COL68; Danio rerio; RNA Seq", "GSM6019653 r1", "GSM6019653", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL68.bam", "bam", 97109456724.0, 558100326.0, "GSM6019653 r1", "0:24 1:150", "A:29936697419;C:20557231468;G:22149381206;T:24410732619;N:55414012", 24, 150, null, null, 29936697419, 20557231468, 22149381206, 24410732619, 55414012, "SRX14746254", "SRS12507761", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00171, 0.64992, 0.00157, 0.07892, 0.99975, 0.8184, 0.41666, 0.55234, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69044, "SRR18643001", "SRX14746253", "SRS12507760", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL67", "GSM6019652", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL67", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019652", "GSM6019652: Micorwell seq datasets of Zebrafish 21d COL67; Danio rerio; RNA Seq", "GSM6019652 r1", "GSM6019652", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL67.bam", "bam", 109862750184.0, 631395116.0, "GSM6019652 r1", "0:24 1:150", "A:33216853380;C:23432599854;G:24752620050;T:28389343698;N:71333202", 24, 150, null, null, 33216853380, 23432599854, 24752620050, 28389343698, 71333202, "SRX14746253", "SRS12507760", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00207, 0.7025, 0.00193, 0.09024, 0.99977, 0.80876, 0.45454, 0.55255, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69045, "SRR18643002", "SRX14746252", "SRS12507758", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL66", "GSM6019651", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL66", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019651", "GSM6019651: Micorwell seq datasets of Zebrafish 21d COL66; Danio rerio; RNA Seq", "GSM6019651 r1", "GSM6019651", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL66.bam", "bam", 109490547306.0, 629256019.0, "GSM6019651 r1", "0:24 1:150", "A:32993927282;C:23470521340;G:24827001184;T:28137815291;N:61282209", 24, 150, null, null, 32993927282, 23470521340, 24827001184, 28137815291, 61282209, "SRX14746252", "SRS12507758", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00195, 0.70435, 0.00184, 0.08444, 0.99983, 0.81065, 0.25, 0.55097, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69046, "SRR18643003", "SRX14746251", "SRS12507759", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL65", "GSM6019650", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d COL65", "Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019650", "GSM6019650: Micorwell seq datasets of Zebrafish 21d COL65; Danio rerio; RNA Seq", "GSM6019650 r1", "GSM6019650", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL65.bam", "bam", 112286603418.0, 645325307.0, "GSM6019650 r1", "0:24 1:150", "A:34447983100;C:24093009711;G:25434725537;T:28237408271;N:73476799", 24, 150, null, null, 34447983100, 24093009711, 25434725537, 28237408271, 73476799, "SRX14746251", "SRS12507759", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00196, 0.68034, 0.00182, 0.07775, 0.99979, 0.82731, 0.3, 0.54802, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69047, "SRR18643004", "SRX14746250", "SRS12507757", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL64", "GSM6019649", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019649", "GSM6019649: Micorwell seq datasets of Zebrafish 21d COL64; Danio rerio; RNA Seq", "GSM6019649 r1", "GSM6019649", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL64.bam", "bam", 92942012304.0, 534149496.0, "GSM6019649 r1", "0:24 1:150", "A:27323539460;C:20109649690;G:21080695471;T:24376651595;N:51476088", 24, 150, null, null, 27323539460, 20109649690, 21080695471, 24376651595, 51476088, "SRX14746250", "SRS12507757", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00161, 0.73948, 0.00154, 0.07949, 0.99989, 0.80957, 0.2, 0.505, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69048, "SRR18643005", "SRX14746249", "SRS12507756", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL63", "GSM6019648", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019648", "GSM6019648: Micorwell seq datasets of Zebrafish 21d COL63; Danio rerio; RNA Seq", "GSM6019648 r1", "GSM6019648", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL63.bam", "bam", 80049514146.0, 460054679.0, "GSM6019648 r1", "0:24 1:150", "A:23166120235;C:17590365167;G:18141366332;T:21101865190;N:49797222", 24, 150, null, null, 23166120235, 17590365167, 18141366332, 21101865190, 49797222, "SRX14746249", "SRS12507756", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00183, 0.75681, 0.00167, 0.07339, 0.99975, 0.8057, 0.38461, 0.50503, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69049, "SRR18643006", "SRX14746248", "SRS12507752", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL62", "GSM6019647", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019647", "GSM6019647: Micorwell seq datasets of Zebrafish 21d COL62; Danio rerio; RNA Seq", "GSM6019647 r1", "GSM6019647", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL62.bam", "bam", 81208183452.0, 466713698.0, "GSM6019647 r1", "0:24 1:150", "A:24295725558;C:17637087135;G:18480719941;T:20751550553;N:43100265", 24, 150, null, null, 24295725558, 17637087135, 18480719941, 20751550553, 43100265, "SRX14746248", "SRS12507752", "SRA1398049", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", "Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine", 2, 0.00198, 0.72047, 0.00187, 0.07058, 0.99981, 0.81724, 0.66666, 0.54415, 24, 150, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-04-05", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [69050, "SRR18643007", "SRX14746247", "SRS12507753", "SRP363983", "PRJNA816047", "Mapping the zebrafish developmental and aging atlas by single cell mRNA seq", "GSE198571", "Transcriptome Analysis", "Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies  we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver  the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here  we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development  maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day  3 replicates  and 10 fish for each replicate and adult 22 month  6 replicates  1 fish for each replicate.", "parent bioproject:PRJNA817101", "pubmed:35929025", null, "Micorwell seq datasets of Zebrafish 21d COL61", "GSM6019646", null, "source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism", "Micorwell seq datasets of Zebrafish 21d 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 in each COL  cellbarcode: in read1  the bases 1 6  22 27  43 48 are merged 18bp; UMI: in read1  the bases 49 54 6bp. For raw file 2 5 in each COL  cellbarcode: in read1  the bases 1 6  7 12  13 18 are merged 18bp; UMI: in read1  the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC  the UMI is tagged with XM  and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts  with genes as rows and cells as columns.", "Zebrafish 21d sample1", null, "Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol", null, "strain:AB|age:21 day|tissue:whole organism", "GSM6019646", "GSM6019646: Micorwell seq datasets of Zebrafish 21d COL61; Danio rerio; RNA Seq", "GSM6019646 r1", "GSM6019646", "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, "SRP363983", null, "assembly:GRCz11|intentional duplicate", "Zebrafish_21d_COL61.bam", "bam", 119375251362.0, 686064663.0, "GSM6019646 r1", "0:24 1:150", "A:36182067005;C:25974297475;G:27163131675;T:29983183018;N:72572189", 24, 150, null, null, 36182067005, 25974297475, 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