{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\" and tissue_curation = \"Gonad\"", "rows": [[52150, "SRR18181456", "SRX14328420", "SRS12144051", "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, "Testis7", "GSM5924294", null, "source name:testis|strain:Tubingen|tissue:testis|genotype:wild type", "Testis7", "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 Mus musculus.GRCm38.88 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.", "testis", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:testis|genotype:wild type", "GSM5924294", "GSM5924294: Testis7; Danio rerio; RNA Seq", "GSM5924294", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM5924294", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10|intentional duplicate", "Testis7.bam", "bam", 22355333400.0, 74517778.0, "GSM5924294 r1", "0:150 1:150", "A:6035271880;C:3425705783;G:3638861956;T:9252935935;N:2557846", 150, 150, null, null, 6035271880, 3425705783, 3638861956, 9252935935, 2557846, "SRX14328420", "SRS12144051", "SRA880843", "GEO", "Zhejiang University", 2, 2e-05, 0.65459, 0.0, 0.06753, 0.99997, 0.78981, 1.0, 0.50866, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52151, "SRR18181455", "SRX14328419", "SRS12144050", "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, "Testis6", "GSM5924293", null, "source name:testis|strain:Tubingen|tissue:testis|genotype:wild type", "Testis6", "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 Mus musculus.GRCm38.88 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.", "testis", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:testis|genotype:wild type", "GSM5924293", "GSM5924293: Testis6; Danio rerio; RNA Seq", "GSM5924293", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM5924293", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10|intentional duplicate", "Testis6.bam", "bam", 26427119100.0, 88090397.0, "GSM5924293 r1", "0:150 1:150", "A:6656757738;C:4332393726;G:4530415358;T:10904715070;N:2837208", 150, 150, null, null, 6656757738, 4332393726, 4530415358, 10904715070, 2837208, "SRX14328419", "SRS12144050", "SRA880843", "GEO", "Zhejiang University", 2, 5e-05, 0.71817, 0.0, 0.06748, 0.99993, 0.78642, 0.66666, 0.5085, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52157, "SRR18181449", "SRX14328413", "SRS12144044", "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, "Ovary5", "GSM5924287", null, "source name:ovary|strain:Tubingen|tissue:ovary|genotype:wild type", "Ovary5", "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 Mus musculus.GRCm38.88 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.", "ovary", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:ovary|genotype:wild type", "GSM5924287", "GSM5924287: Ovary5; Danio rerio; RNA Seq", "GSM5924287", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM5924287", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10|intentional duplicate", "Ovary5.bam", "bam", 19803996900.0, 66013323.0, "GSM5924287 r1", "0:150 1:150", "A:5073828462;C:3239587102;G:3356397736;T:8132061615;N:2121985", 150, 150, null, null, 5073828462, 3239587102, 3356397736, 8132061615, 2121985, "SRX14328413", "SRS12144044", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.69276, 0.0, 0.03046, 1.0, 0.8297, null, 0.5054, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52158, "SRR18181448", "SRX14328412", "SRS12144043", "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, "Ovary4", "GSM5924286", null, "source name:ovary|strain:Tubingen|tissue:ovary|genotype:wild type", "Ovary4", "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 Mus musculus.GRCm38.88 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.", "ovary", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:ovary|genotype:wild type", "GSM5924286", "GSM5924286: Ovary4; Danio rerio; RNA Seq", "GSM5924286", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM5924286", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10|intentional duplicate", "Ovary4.bam", "bam", 18909491400.0, 63031638.0, "GSM5924286 r1", "0:150 1:150", "A:4449523781;C:3271362982;G:3415526983;T:7771066311;N:2011343", 150, 150, null, null, 4449523781, 3271362982, 3415526983, 7771066311, 2011343, "SRX14328412", "SRS12144043", "SRA880843", "GEO", "Zhejiang University", 2, 2e-05, 0.80325, 0.0, 0.03273, 0.99997, 0.81895, 1.0, 0.53235, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52181, "SRR9058966", "SRX5835166", "SRS4761462", "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, "Testis2", "GSM3768163", null, "source name:testis|strain:Tubingen|genotype/variation:wild type|tissue:testis", "Testis2", "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.", "testis", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:testis", "GSM3768163", "GSM3768163: Testis2; Danio rerio; RNA Seq", "GSM3768163", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Testis2.bam", "bam", 10897833300.0, 36326111.0, "GSM3768163 r1", "0:150 1:150", "A:2949189012;C:1827068947;G:1843781525;T:4276886403;N:907413", 150, 150, null, null, 2949189012, 1827068947, 1843781525, 4276886403, 907413, "SRX5835166", "SRS4761462", "SRA880843", "GEO", "Zhejiang University", 2, 5e-05, 0.72733, 1e-05, 0.0449, 0.99995, 0.78216, 0.5, 0.50959, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52182, "SRR9058965", "SRX5835165", "SRS4761461", "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, "Testis1", "GSM3768162", null, "source name:testis|strain:Tubingen|genotype/variation:wild type|tissue:testis", "Testis1", "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.", "testis", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:testis", "GSM3768162", "GSM3768162: Testis1; Danio rerio; RNA Seq", "GSM3768162", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768162", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Testis1.bam", "bam", 20087467800.0, 66958226.0, "GSM3768162 r1", "0:150 1:150", "A:5333777727;C:3476144155;G:3519583110;T:7754981380;N:2981428", 150, 150, null, null, 5333777727, 3476144155, 3519583110, 7754981380, 2981428, "SRX5835165", "SRS4761461", "SRA880843", "GEO", "Zhejiang University", 2, 3e-05, 0.71273, 0.0, 0.05569, 0.99997, 0.78151, 1.0, 0.49988, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52183, "SRR9058964", "SRX5835164", "SRS4761460", "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, "Ovary2", "GSM3768161", null, "source name:ovary|strain:Tubingen|genotype/variation:wild type|tissue:ovary", "Ovary2", "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.", "ovary", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:ovary", "GSM3768161", "GSM3768161: Ovary2; Danio rerio; RNA Seq", "GSM3768161", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Ovary2.bam", "bam", 27873510686.0, 92296393.0, "GSM3768161 r1", "0:151 1:151", "A:7431755509;C:4813567006;G:4753054905;T:10804284010;N:70849256", 151, 151, null, null, 7431755509, 4813567006, 4753054905, 10804284010, 70849256, "SRX5835164", "SRS4761460", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.64422, 0.0, 0.03306, 1.0, 0.85251, null, 0.49446, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52198, "SRR8991408", "SRX5770476", "SRS4704585", "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, "Testis5", "GSM3740961", null, "source name:testis|strain:Tubingen|genotype:wild type|tissue:testis", "Testis5", "The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. 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: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index 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.", "testis", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype:wild type|tissue:testis", "GSM3740961", "GSM3740961: Testis5; Danio rerio; RNA Seq", "GSM3740961", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3740961", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10", "Testis5.bam", "bam", 25120411340.0, 83180170.0, "GSM3740961 r1", "0:151 1:151", "A:6309984521;C:4265951177;G:4463773513;T:10013679424;N:67022705", 151, 151, null, null, 6309984521, 4265951177, 4463773513, 10013679424, 67022705, "SRX5770476", "SRS4704585", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.73589, 0.0, 0.05677, 1.0, 0.76852, null, 0.48176, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-04-30", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [52202, "SRR8991404", "SRX5770472", "SRS4704581", "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, "Ovary3", "GSM3740957", null, "source name:ovary|strain:Tubingen|genotype:wild type|tissue:ovary", "Ovary3", "The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. 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: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index 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.", "ovary", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype:wild type|tissue:ovary", "GSM3740957", "GSM3740957: Ovary3; Danio rerio; RNA Seq", "GSM3740957", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3740957", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:Danio rerio GRCz10", "Ovary3.bam", "bam", 28925343900.0, 96417813.0, "GSM3740957 r1", "0:150 1:150", "A:7017871289;C:5039388405;G:5052960907;T:11812448419;N:2674880", 150, 150, null, null, 7017871289, 5039388405, 5052960907, 11812448419, 2674880, "SRX5770472", "SRS4704581", "SRA880843", "GEO", "Zhejiang University", 2, 2e-05, 0.79333, 0.0, 0.03249, 0.99997, 0.83374, 0.0, 0.48484, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-04-30", "Undetermined", "Multi-stage", "Gonad", "Reproductive System"], [68556, "SRR18028171", "SRX14182301", "SRS12005942", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "6WT 3", null, "strain:AB|isolate:replicate3|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 3 S11 L001 R1", "011", "011", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz", "fastq fastq", 3576981600.0, 11923272.0, "wt 3 S11 L001 R1 001.fastq.gz", "0:150 1:150", "A:689001630;C:496844981;G:1779990511;T:610974133;N:170345", 150, 150, null, null, 689001630, 496844981, 1779990511, 610974133, 170345, "SRX14182301", "SRS12005942", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.8179, 0.81697, 0.60905, 0.60864, 0.82692, 0.82915, 0.52425, 0.52623, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68557, "SRR18028172", "SRX14182300", "SRS12005941", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "5WT 2", null, "strain:AB|isolate:replicate2|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 2 S10 L001 R1", "009", "009", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz", "fastq fastq", 4200013800.0, 14000046.0, "wt 2 S10 L001 R1 001.fastq.gz", "0:150 1:150", "A:781057232;C:617020885;G:2110010128;T:691723797;N:201758", 150, 150, null, null, 781057232, 617020885, 2110010128, 691723797, 201758, "SRX14182300", "SRS12005941", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.8213, 0.82216, 0.59414, 0.59507, 0.81089, 0.81306, 0.53839, 0.52755, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68558, "SRR18028173", "SRX14182299", "SRS12005940", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "4WT 1", null, "strain:AB|isolate:replicate1|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 1 S9 L001 R1", "007", "007", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz", "fastq fastq", 4820063700.0, 16066879.0, "wt 1 S9 L001 R1 001.fastq.gz", "0:150 1:150", "A:996304548;C:657334691;G:2379519106;T:786675131;N:230224", 150, 150, null, null, 996304548, 657334691, 2379519106, 786675131, 230224, "SRX14182299", "SRS12005940", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.80219, 0.80319, 0.60906, 0.60878, 0.83238, 0.83303, 0.52559, 0.51852, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68559, "SRR18028174", "SRX14182298", "SRS12005939", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "3PLD6 3", null, "strain:AB|isolate:replicate3|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 3 S3 L003 R1", "005", "005", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz", "fastq fastq", 816686700.0, 2722289.0, "pld6 3 S3 L003 R1 001.fastq.gz", "0:150 1:150", "A:145681738;C:137123477;G:401610833;T:132256312;N:14340", 150, 150, null, null, 145681738, 137123477, 401610833, 132256312, 14340, "SRX14182298", "SRS12005939", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.78314, 0.73942, 0.07641, 0.09097, 0.91603, 0.91545, 0.6312, 0.64467, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68560, "SRR18028175", "SRX14182297", "SRS12005938", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "2PLD6 2", null, "strain:AB|isolate:replicate2|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 2 S2 L003 R1", "003", "003", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz", "fastq fastq", 6546276900.0, 21820923.0, "pld6 2 S2 L003 R1 001.fastq.gz", "0:150 1:150", "A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957", 150, 150, null, null, 1161502458, 1095580994, 3226725392, 1062358099, 109957, "SRX14182297", "SRS12005938", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.6471, 0.593, 0.07935, 0.09168, 0.92058, 0.92005, 0.53626, 0.65284, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68561, "SRR18028176", "SRX14182296", "SRS12005937", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "1PLD6 1", null, "strain:AB|isolate:replicate1|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 1 S1 L003 R1", "001", "001", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz", "fastq fastq", 5535130200.0, 18450434.0, "pld6 1 S1 L003 R1 001.fastq.gz", "0:150 1:150", "A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680", 150, 150, null, null, 1014761790, 833992394, 2813863824, 872418512, 93680, "SRX14182296", "SRS12005937", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.70358, 0.73288, 0.08649, 0.09366, 0.91066, 0.90914, 0.6197, 0.6207, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [77261, "SRR25434203", "SRX21168298", "SRS18429832", "SRP451673", "PRJNA999043", "The transcription analysis of gonad in zebrafish", "PRJNA999043", "Other", "To screen out the female biased genes", null, null, null, null, "dmrt / 2", null, "isolate:not applicable|age:80days|dev stage:Adult|collection date:2021|geo loc name:China:Wuhan|sex:female|tissue:Gonad|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of gonad", "dmrt2", "dmrt2", "screen out the key genes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451673", null, null, "dmrt2_R1_.fastq.gz dmrt2_R2.fastq.gz", "fastq fastq", 5751045000.0, 19170150.0, "dmrt2 R1 .fastq.gz", "0:150 1:150", "A:1488645455;C:1371887358;G:1405356847;T:1485112991;N:42349", 150, 150, null, null, 1488645455, 1371887358, 1405356847, 1485112991, 42349, "SRX21168298", "SRS18429832", "SRA1681175", "Chinese Academy of Sciences|Institute of Hydrology", "Chinese Academy of Sciences", 2, 0.91589, 0.91745, 0.01703, 0.01705, 0.7637, 0.76402, 0.47113, 0.46945, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-27", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [77262, "SRR25434204", "SRX21168297", "SRS18429831", "SRP451673", "PRJNA999043", "The transcription analysis of gonad in zebrafish", "PRJNA999043", "Other", "To screen out the female biased genes", null, null, null, null, "dmrt / 1", null, "isolate:not applicable|age:80days|dev stage:Adult|collection date:2021|geo loc name:China:Wuhan|sex:female|tissue:Gonad|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of gonad", "dmrt1", "dmrt1", "screen out the key genes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451673", null, null, "dmrt1_R2.fastq.gz dmrt1_R1.fastq.gz", "fastq fastq", 7183531200.0, 23945104.0, "dmrt1 R1.fastq.gz", "0:150 1:150", "A:1847909835;C:1724710101;G:1769658622;T:1841199904;N:52738", 150, 150, null, null, 1847909835, 1724710101, 1769658622, 1841199904, 52738, "SRX21168297", "SRS18429831", "SRA1681175", "Chinese Academy of Sciences|Institute of Hydrology", "Chinese Academy of Sciences", 2, 0.92259, 0.92339, 0.01692, 0.01663, 0.76558, 0.76589, 0.46917, 0.46678, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-27", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [77263, "SRR25434205", "SRX21168296", "SRS18429830", "SRP451673", "PRJNA999043", "The transcription analysis of gonad in zebrafish", "PRJNA999043", "Other", "To screen out the female biased genes", null, null, null, null, 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"novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-27", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [77264, "SRR25434206", "SRX21168295", "SRS18429829", "SRP451673", "PRJNA999043", "The transcription analysis of gonad in zebrafish", "PRJNA999043", "Other", "To screen out the female biased genes", null, null, null, null, "cyp17a1 / ;dmrt1 / 1", null, "isolate:not applicable|age:80days|dev stage:Adult|collection date:2021|geo loc name:China:Wuhan|sex:female|tissue:Gonad|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of gonad", "dko1", "dko1", "screen out the key genes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451673", null, null, "dko1_R1.fastq.gz dko1_R2.fastq.gz", "fastq fastq", 6638354100.0, 22127847.0, "dko1 R1.fastq.gz", "0:150 1:150", 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