rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 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.,,pubmed:34660600,,Testis7,GSM5924294,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:testis|genotype:wild type,GSM5924294,GSM5924294: Testis7; Danio rerio; RNA Seq,GSM5924294,,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,,SRP194254,,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,,,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,,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.,,pubmed:34660600,,Testis6,GSM5924293,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:testis|genotype:wild type,GSM5924293,GSM5924293: Testis6; Danio rerio; RNA Seq,GSM5924293,,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,,SRP194254,,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,,,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,,China,2022-03-01,Undetermined,Multi-stage,Gonad,Reproductive System 52152,SRR18181454,SRX14328418,SRS12144049,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder3,GSM5924292,,source name:swim bladder|strain:Tubingen|tissue:swim bladder|genotype:wild type,Swim Bladder3,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.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:swim bladder|genotype:wild type,GSM5924292,GSM5924292: Swim Bladder3; Danio rerio; RNA Seq,GSM5924292,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924292,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,SwimBladder3.bam,bam,45191935800.0,150639786.0,GSM5924292 r1,0:150 1:150,A:10476251757;C:8049557401;G:8173647398;T:18490392981;N:2086263,150,150,,,10476251757,8049557401,8173647398,18490392981,2086263,SRX14328418,SRS12144049,SRA880843,GEO,Zhejiang University,2,0.0,0.76544,0.0,0.02769,1.0,0.86291,,0.51073,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Swim Bladder,Swim Bladder 52153,SRR18181453,SRX14328417,SRS12144048,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder2,GSM5924291,,source name:swim bladder|strain:Tubingen|tissue:swim bladder|genotype:wild type,Swim Bladder2,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.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:swim bladder|genotype:wild type,GSM5924291,GSM5924291: Swim Bladder2; Danio rerio; RNA Seq,GSM5924291,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924291,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,SwimBladder2.bam,bam,18824466944.0,62332672.0,GSM5924291 r1,0:151 1:151,A:4604254176;C:3130145977;G:3233969707;T:7851792248;N:4304836,151,151,,,4604254176,3130145977,3233969707,7851792248,4304836,SRX14328417,SRS12144048,SRA880843,GEO,Zhejiang University,2,0.0,0.75695,0.0,0.03113,1.0,0.84346,,0.54953,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Swim Bladder,Swim Bladder 52154,SRR18181452,SRX14328416,SRS12144047,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin6,GSM5924290,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin6,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.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924290,GSM5924290: Skin6; Danio rerio; RNA Seq,GSM5924290,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924290,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin6.bam,bam,25513490100.0,85044967.0,GSM5924290 r1,0:150 1:150,A:6925113942;C:3968740165;G:4171395948;T:10445470654;N:2769391,150,150,,,6925113942,3968740165,4171395948,10445470654,2769391,SRX14328416,SRS12144047,SRA880843,GEO,Zhejiang University,2,2e-05,0.59157,0.0,0.06443,0.99997,0.87677,1.0,0.63522,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 52155,SRR18181451,SRX14328415,SRS12144046,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin5,GSM5924289,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin5,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.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924289,GSM5924289: Skin5; Danio rerio; RNA Seq,GSM5924289,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin5.bam,bam,28489208700.0,94964029.0,GSM5924289 r1,0:150 1:150,A:8246685822;C:4290659458;G:4422543987;T:11526089448;N:3229985,150,150,,,8246685822,4290659458,4422543987,11526089448,3229985,SRX14328415,SRS12144046,SRA880843,GEO,Zhejiang University,2,0.0,0.52,0.0,0.05199,1.0,0.89509,,0.61209,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 52156,SRR18181450,SRX14328414,SRS12144045,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin3,GSM5924288,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin3,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.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924288,GSM5924288: Skin3; Danio rerio; RNA Seq,GSM5924288,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin3.bam,bam,22656818700.0,75522729.0,GSM5924288 r1,0:150 1:150,A:5656101080;C:3775541088;G:3901788913;T:9321421770;N:1965849,150,150,,,5656101080,3775541088,3901788913,9321421770,1965849,SRX14328414,SRS12144045,SRA880843,GEO,Zhejiang University,2,2e-05,0.77804,0.0,0.0376,0.99997,0.77275,1.0,0.58426,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 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.,,pubmed:34660600,,Ovary5,GSM5924287,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:ovary|genotype:wild type,GSM5924287,GSM5924287: Ovary5; Danio rerio; RNA Seq,GSM5924287,,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,,SRP194254,,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,,,5073828462,3239587102,3356397736,8132061615,2121985,SRX14328413,SRS12144044,SRA880843,GEO,Zhejiang University,2,0.0,0.69276,0.0,0.03046,1.0,0.8297,,0.5054,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,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.,,pubmed:34660600,,Ovary4,GSM5924286,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:ovary|genotype:wild type,GSM5924286,GSM5924286: Ovary4; Danio rerio; RNA Seq,GSM5924286,,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,,SRP194254,,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,,,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,,China,2022-03-01,Undetermined,Multi-stage,Gonad,Reproductive System 52159,SRR18181447,SRX14328411,SRS12144042,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Liver7,GSM5924285,,source name:liver|strain:Tubingen|tissue:liver|genotype:wild type,Liver7,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.,liver,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:liver|genotype:wild type,GSM5924285,GSM5924285: Liver7; Danio rerio; RNA Seq,GSM5924285,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924285,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Liver7.bam,bam,27939998700.0,93133329.0,GSM5924285 r1,0:150 1:150,A:7395587537;C:4460827164;G:4658709882;T:11421741087;N:3133030,150,150,,,7395587537,4460827164,4658709882,11421741087,3133030,SRX14328411,SRS12144042,SRA880843,GEO,Zhejiang University,2,2e-05,0.65679,1e-05,0.04023,1.0,0.87746,,0.58048,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Liver,Liver and Biliary System 52160,SRR18181446,SRX14328410,SRS12144041,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Liver6,GSM5924284,,source name:liver|strain:Tubingen|tissue:liver|genotype:wild type,Liver6,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.,liver,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:liver|genotype:wild type,GSM5924284,GSM5924284: Liver6; Danio rerio; RNA Seq,GSM5924284,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924284,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Liver6.bam,bam,22968934500.0,76563115.0,GSM5924284 r1,0:150 1:150,A:6159445676;C:3639426657;G:3793850765;T:9373594248;N:2617154,150,150,,,6159445676,3639426657,3793850765,9373594248,2617154,SRX14328410,SRS12144041,SRA880843,GEO,Zhejiang University,2,0.0,0.63504,0.0,0.03827,1.0,0.88596,,0.54699,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Liver,Liver and Biliary System 52161,SRR18181445,SRX14328409,SRS12144040,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Intestine7,GSM5924283,,source name:intestinePancreas|strain:Tubingen|tissue:intestinePancreas|genotype:wild type,Intestine7,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.,intestinePancreas,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:intestinePancreas|genotype:wild type,GSM5924283,GSM5924283: Intestine7; Danio rerio; RNA Seq,GSM5924283,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924283,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Intestine7.bam,bam,22400996700.0,74669989.0,GSM5924283 r1,0:150 1:150,A:5884891821;C:3619736493;G:3679703893;T:9214284747;N:2379746,150,150,,,5884891821,3619736493,3679703893,9214284747,2379746,SRX14328409,SRS12144040,SRA880843,GEO,Zhejiang University,2,0.0,0.6961,0.0,0.0336,1.0,0.85675,,0.54738,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Multi-tissue,Multi-system 52162,SRR18181444,SRX14328408,SRS12144039,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Intestine6,GSM5924282,,source name:intestinePancreas|strain:Tubingen|tissue:intestinePancreas|genotype:wild type,Intestine6,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.,intestinePancreas,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:intestinePancreas|genotype:wild type,GSM5924282,GSM5924282: Intestine6; Danio rerio; RNA Seq,GSM5924282,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924282,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Intestine6.bam,bam,16871120400.0,56237068.0,GSM5924282 r1,0:150 1:150,A:4384014639;C:2824145389;G:2880732221;T:6780420013;N:1808138,150,150,,,4384014639,2824145389,2880732221,6780420013,1808138,SRX14328408,SRS12144039,SRA880843,GEO,Zhejiang University,2,0.0,0.74504,0.0,0.03583,1.0,0.85616,,0.55616,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Multi-tissue,Multi-system 52163,SRR18181443,SRX14328407,SRS12144038,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Heart2,GSM5924281,,source name:heart|strain:Tubingen|tissue:heart|genotype:wild type,Heart2,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.,heart,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:heart|genotype:wild type,GSM5924281,GSM5924281: Heart2; Danio rerio; RNA Seq,GSM5924281,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924281,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Heart2.bam,bam,12289381500.0,40964605.0,GSM5924281 r1,0:150 1:150,A:2992562186;C:2244952830;G:2193151336;T:4856123220;N:2591928,150,150,,,2992562186,2244952830,2193151336,4856123220,2591928,SRX14328407,SRS12144038,SRA880843,GEO,Zhejiang University,2,0.0,0.78893,0.0,0.01228,1.0,0.91441,,0.62655,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Heart,Cardiovascular System 52164,SRR18181442,SRX14328406,SRS12144037,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Heart1,GSM5924280,,source name:heart|strain:Tubingen|tissue:heart|genotype:wild type,Heart1,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.,heart,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:heart|genotype:wild type,GSM5924280,GSM5924280: Heart1; Danio rerio; RNA Seq,GSM5924280,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924280,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Heart1.bam,bam,8428658100.0,28095527.0,GSM5924280 r1,0:150 1:150,A:2058121249;C:1561350035;G:1570099343;T:3238195048;N:892425,150,150,,,2058121249,1561350035,1570099343,3238195048,892425,SRX14328406,SRS12144037,SRA880843,GEO,Zhejiang University,2,2e-05,0.88435,0.0,0.01173,0.99997,0.89045,1.0,0.54187,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Heart,Cardiovascular System 52165,SRR18181441,SRX14328405,SRS12144036,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Gill6,GSM5924279,,source name:gill|strain:Tubingen|tissue:gill|genotype:wild type,Gill6,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.,gill,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:gill|genotype:wild type,GSM5924279,GSM5924279: Gill6; Danio rerio; RNA Seq,GSM5924279,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924279,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Gill6.bam,bam,19809945600.0,66033152.0,GSM5924279 r1,0:150 1:150,A:5239766235;C:3329504882;G:3343228185;T:7895078269;N:2368029,150,150,,,5239766235,3329504882,3343228185,7895078269,2368029,SRX14328405,SRS12144036,SRA880843,GEO,Zhejiang University,2,0.0,0.70563,0.0,0.05162,1.0,0.8565,,0.67358,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Gill,Respiratory System 52166,SRR18181440,SRX14328404,SRS12144035,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Gill5,GSM5924278,,source name:gill|strain:Tubingen|tissue:gill|genotype:wild type,Gill5,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.,gill,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:gill|genotype:wild type,GSM5924278,GSM5924278: Gill5; Danio rerio; RNA Seq,GSM5924278,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924278,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Gill5.bam,bam,21230554200.0,70768514.0,GSM5924278 r1,0:150 1:150,A:5525026007;C:3634039752;G:3645652541;T:8423300924;N:2534976,150,150,,,5525026007,3634039752,3645652541,8423300924,2534976,SRX14328404,SRS12144035,SRA880843,GEO,Zhejiang University,2,2e-05,0.7412,0.0,0.05354,0.99997,0.85462,0.0,0.66686,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Gill,Respiratory System 52167,SRR18181439,SRX14328403,SRS12144034,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Gill3,GSM5924277,,source name:gill|strain:Tubingen|tissue:gill|genotype:wild type,Gill3,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.,gill,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:gill|genotype:wild type,GSM5924277,GSM5924277: Gill3; Danio rerio; RNA Seq,GSM5924277,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924277,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Gill3.bam,bam,21579822900.0,71932743.0,GSM5924277 r1,0:150 1:150,A:5441997035;C:3521528250;G:3625669551;T:8988770258;N:1857806,150,150,,,5441997035,3521528250,3625669551,8988770258,1857806,SRX14328403,SRS12144034,SRA880843,GEO,Zhejiang University,2,0.0,0.74255,0.0,0.03463,1.0,0.81434,,0.586,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Gill,Respiratory System 52168,SRR18181438,SRX14328402,SRS12144033,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Eye3,GSM5924276,,source name:eye|strain:Tubingen|tissue:eye|genotype:wild type,Eye3,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.,eye,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:eye|genotype:wild type,GSM5924276,GSM5924276: Eye3; Danio rerio; RNA Seq,GSM5924276,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924276,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Eye3.bam,bam,15432297300.0,51440991.0,GSM5924276 r1,0:150 1:150,A:4354553670;C:2433124600;G:2447610770;T:6195160523;N:1847737,150,150,,,4354553670,2433124600,2447610770,6195160523,1847737,SRX14328402,SRS12144033,SRA880843,GEO,Zhejiang University,2,5e-05,0.60307,4e-05,0.06123,1.0,0.86265,,0.57125,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Eye,Sensory System 52173,SRR10902874,SRX7571044,SRS6006645,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,muscle 2,GSM4274620,,source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type,muscle 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.,muscle,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:muscle|genotype:wild type,GSM4274620,GSM4274620: muscle 2; Danio rerio; RNA Seq,GSM4274620,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274620,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,muscle2.bam,bam,16930081042.0,56059871.0,GSM4274620 r1,0:151 1:151,A:4603243415;C:3058165767;G:2976076252;T:6287916322;N:4679286,151,151,,,4603243415,3058165767,2976076252,6287916322,4679286,SRX7571044,SRS6006645,SRA880843,GEO,Zhejiang University,2,3e-05,0.62236,0.0,0.0478,0.99997,0.86547,1.0,0.64653,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Muscle,Muscular System 52174,SRR10902873,SRX7571043,SRS6006644,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,muscle 1,GSM4274619,,source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type,muscle 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.,muscle,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:muscle|genotype:wild type,GSM4274619,GSM4274619: muscle 1; Danio rerio; RNA Seq,GSM4274619,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274619,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,muscle1.bam,bam,16720405462.0,55365581.0,GSM4274619 r1,0:151 1:151,A:4156663457;C:3083564895;G:3052902778;T:6423378000;N:3896332,151,151,,,4156663457,3083564895,3052902778,6423378000,3896332,SRX7571043,SRS6006644,SRA880843,GEO,Zhejiang University,2,0.0,0.65433,0.0,0.02201,1.0,0.88237,,0.6721,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Muscle,Muscular System 52175,SRR10902872,SRX7571042,SRS6006643,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Blood 2,GSM4274618,,source name:blood|strain:Tubingen|tissue:blood|genotype:wild type,Blood 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.,blood,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:blood|genotype:wild type,GSM4274618,GSM4274618: Blood 2; Danio rerio; RNA Seq,GSM4274618,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274618,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,Blood2.bam,bam,31418773850.0,104035675.0,GSM4274618 r1,0:151 1:151,A:8027580943;C:5644210831;G:5587896051;T:12151089233;N:7996792,151,151,,,8027580943,5644210831,5587896051,12151089233,7996792,SRX7571042,SRS6006643,SRA880843,GEO,Zhejiang University,2,8e-05,0.56276,0.0,0.04786,0.99991,0.88363,0.75,0.53078,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Blood,Hematopoietic System 52176,SRR10902871,SRX7571041,SRS6006642,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Blood 1,GSM4274617,,source name:blood|strain:Tubingen|tissue:blood|genotype:wild type,Blood 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.,blood,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:blood|genotype:wild type,GSM4274617,GSM4274617: Blood 1; Danio rerio; RNA Seq,GSM4274617,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274617,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,Blood1.bam,bam,14970178354.0,49570127.0,GSM4274617 r1,0:151 1:151,A:3767585238;C:2725333545;G:2707312228;T:5766389198;N:3558145,151,151,,,3767585238,2725333545,2707312228,5766389198,3558145,SRX7571041,SRS6006642,SRA880843,GEO,Zhejiang University,2,0.0,0.58542,0.0,0.0298,1.0,0.89033,,0.53826,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Blood,Hematopoietic System 52177,SRR10902870,SRX7571040,SRS6006641,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin 6,GSM4274616,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 6,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274616,GSM4274616: CaudalFin 6; Danio rerio; RNA Seq,GSM4274616,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274616,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin6.bam,bam,15182183400.0,50607278.0,GSM4274616 r1,0:150 1:150,A:3885671292;C:2808118660;G:2749433455;T:5736812768;N:2147225,150,150,,,3885671292,2808118660,2749433455,5736812768,2147225,SRX7571040,SRS6006641,SRA880843,GEO,Zhejiang University,2,0.0,0.75585,0.0,0.03963,1.0,0.85683,,0.66839,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure 52178,SRR10902869,SRX7571039,SRS6006640,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin 5,GSM4274615,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 5,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274615,GSM4274615: CaudalFin 5; Danio rerio; RNA Seq,GSM4274615,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274615,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin5.bam,bam,12714687300.0,42382291.0,GSM4274615 r1,0:150 1:150,A:3251897336;C:2310288259;G:2258210415;T:4892500201;N:1791089,150,150,,,3251897336,2310288259,2258210415,4892500201,1791089,SRX7571039,SRS6006640,SRA880843,GEO,Zhejiang University,2,0.0,0.72038,0.0,0.03882,1.0,0.86032,,0.62044,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure 52179,SRR10902868,SRX7571038,SRS6006639,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin 4,GSM4274614,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 4,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274614,GSM4274614: CaudalFin 4; Danio rerio; RNA Seq,GSM4274614,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274614,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin4.bam,bam,11693371200.0,38977904.0,GSM4274614 r1,0:150 1:150,A:3057191149;C:2115231923;G:2060789562;T:4458505458;N:1653108,150,150,,,3057191149,2115231923,2060789562,4458505458,1653108,SRX7571038,SRS6006639,SRA880843,GEO,Zhejiang University,2,0.0,0.69243,0.0,0.02868,1.0,0.86801,,0.58425,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure 52180,SRR10902867,SRX7571037,SRS6006638,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin 3,GSM4274613,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 3,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274613,GSM4274613: CaudalFin 3; Danio rerio; RNA Seq,GSM4274613,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274613,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin3.bam,bam,15450513000.0,51501710.0,GSM4274613 r1,0:150 1:150,A:4147311733;C:2703423917;G:2642017355;T:5955551498;N:2208497,150,150,,,4147311733,2703423917,2642017355,5955551498,2208497,SRX7571037,SRS6006638,SRA880843,GEO,Zhejiang University,2,3e-05,0.65311,0.0,0.03421,0.99997,0.8774,0.0,0.57684,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure 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.,,pubmed:34660600,,Testis2,GSM3768163,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:testis,GSM3768163,GSM3768163: Testis2; Danio rerio; RNA Seq,GSM3768163,,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,,SRP194254,,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,,,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,,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.,,pubmed:34660600,,Testis1,GSM3768162,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:testis,GSM3768162,GSM3768162: Testis1; Danio rerio; RNA Seq,GSM3768162,,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,,SRP194254,,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,,,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,,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.,,pubmed:34660600,,Ovary2,GSM3768161,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:ovary,GSM3768161,GSM3768161: Ovary2; Danio rerio; RNA Seq,GSM3768161,,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,,SRP194254,,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,,,7431755509,4813567006,4753054905,10804284010,70849256,SRX5835164,SRS4761460,SRA880843,GEO,Zhejiang University,2,0.0,0.64422,0.0,0.03306,1.0,0.85251,,0.49446,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Gonad,Reproductive System 52184,SRR9058963,SRX5835163,SRS4761459,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Muscle2,GSM3768160,,source name:muscle|strain:Tubingen|genotype/variation:wild type|tissue:muscle,Muscle2,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.,muscle,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:muscle,GSM3768160,GSM3768160: Muscle2; Danio rerio; RNA Seq,GSM3768160,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768160,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Muscle2.bam,bam,23974175100.0,79913917.0,GSM3768160 r1,0:150 1:150,A:5944663891;C:3921811959;G:4069898582;T:10035651088;N:2149580,150,150,,,5944663891,3921811959,4069898582,10035651088,2149580,SRX5835163,SRS4761459,SRA880843,GEO,Zhejiang University,2,0.0,0.73445,0.0,0.02498,1.0,0.85267,,0.59746,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Muscle,Muscular System 52185,SRR9058962,SRX5835162,SRS4761458,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Liver4,GSM3768159,,source name:liver|strain:Tubingen|genotype/variation:wild type|tissue:liver,Liver4,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.,liver,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:liver,GSM3768159,GSM3768159: Liver4; Danio rerio; RNA Seq,GSM3768159,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768159,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Liver4.bam,bam,10631865002.0,35204851.0,GSM3768159 r1,0:151 1:151,A:2648862091;C:1782607746;G:1796901940;T:4375340137;N:28153088,151,151,,,2648862091,1782607746,1796901940,4375340137,28153088,SRX5835162,SRS4761458,SRA880843,GEO,Zhejiang University,2,0.0,0.75662,0.0,0.012,1.0,0.9175,,0.55732,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Liver,Liver and Biliary System 52186,SRR9058961,SRX5835161,SRS4761457,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Intestine4,GSM3768158,,source name:intestinePancreas|strain:Tubingen|genotype/variation:wild type|tissue:intestinePancreas,Intestine4,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.,intestinePancreas,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:intestinePancreas,GSM3768158,GSM3768158: Intestine4; Danio rerio; RNA Seq,GSM3768158,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768158,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Intestine4.bam,bam,9566569968.0,31677384.0,GSM3768158 r1,0:151 1:151,A:2586362813;C:1520597961;G:1544487744;T:3890395722;N:24725728,151,151,,,2586362813,1520597961,1544487744,3890395722,24725728,SRX5835161,SRS4761457,SRA880843,GEO,Zhejiang University,2,0.0,0.64605,0.0,0.02101,1.0,0.86811,,0.57648,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Multi-tissue,Multi-system 52187,SRR9058960,SRX5835160,SRS4761456,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Intestine3,GSM3768157,,source name:intestinePancreas|strain:Tubingen|genotype/variation:wild type|tissue:intestinePancreas,Intestine3,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.,intestinePancreas,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:intestinePancreas,GSM3768157,GSM3768157: Intestine3; Danio rerio; RNA Seq,GSM3768157,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768157,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Intestine3.bam,bam,21883094400.0,72943648.0,GSM3768157 r1,0:150 1:150,A:5262875683;C:3798642011;G:3894815542;T:8924899880;N:1861284,150,150,,,5262875683,3798642011,3894815542,8924899880,1861284,SRX5835160,SRS4761456,SRA880843,GEO,Zhejiang University,2,2e-05,0.77407,1e-05,0.00958,1.0,0.88889,,0.5577,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Multi-tissue,Multi-system 52188,SRR9058959,SRX5835159,SRS4761455,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Heart4,GSM3768156,,source name:heart|strain:Tubingen|genotype/variation:wild type|tissue:heart,Heart4,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.,heart,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:heart,GSM3768156,GSM3768156: Heart4; Danio rerio; RNA Seq,GSM3768156,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768156,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Heart4.bam,bam,52461585418.0,173713859.0,GSM3768156 r1,0:151 1:151,A:12784605546;C:9053648554;G:9236590524;T:21249234138;N:137506656,151,151,,,12784605546,9053648554,9236590524,21249234138,137506656,SRX5835159,SRS4761455,SRA880843,GEO,Zhejiang University,2,0.0,0.77522,0.0,0.03304,1.0,0.85632,,0.55248,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Heart,Cardiovascular System 52189,SRR9058958,SRX5835158,SRS4761454,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Heart3,GSM3768155,,source name:heart|strain:Tubingen|genotype/variation:wild type|tissue:heart,Heart3,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.,heart,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:heart,GSM3768155,GSM3768155: Heart3; Danio rerio; RNA Seq,GSM3768155,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768155,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Heart3.bam,bam,23533995978.0,77927139.0,GSM3768155 r1,0:151 1:151,A:6051087690;C:3978622675;G:3909835641;T:9588867829;N:5582143,151,151,,,6051087690,3978622675,3909835641,9588867829,5582143,SRX5835158,SRS4761454,SRA880843,GEO,Zhejiang University,2,0.0,0.74298,0.0,0.02452,1.0,0.88107,,0.61909,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Heart,Cardiovascular System 52190,SRR9058957,SRX5835157,SRS4761453,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Eye1,GSM3768154,,source name:eye|strain:Tubingen|genotype/variation:wild type|tissue:eye,Eye1,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.,eye,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:eye,GSM3768154,GSM3768154: Eye1; Danio rerio; RNA Seq,GSM3768154,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768154,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Eye1.bam,bam,37155841274.0,123032587.0,GSM3768154 r1,0:151 1:151,A:9138846228;C:6458258540;G:6507520861;T:15044585234;N:6630411,151,151,,,9138846228,6458258540,6507520861,15044585234,6630411,SRX5835157,SRS4761453,SRA880843,GEO,Zhejiang University,2,2e-05,0.84079,0.0,0.04869,0.99997,0.84167,0.0,0.66089,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Eye,Sensory System 52191,SRR9058956,SRX5835156,SRS4761452,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin1,GSM3768153,,source name:caudal fin|strain:Tubingen|genotype/variation:wild type|tissue:caudal fin,CaudalFin1,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:caudal fin,GSM3768153,GSM3768153: CaudalFin1; Danio rerio; RNA Seq,GSM3768153,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768153,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,CaudalFin1.bam,bam,14329147114.0,47447507.0,GSM3768153 r1,0:151 1:151,A:3440675044;C:2610927283;G:2684180140;T:5590878261;N:2486386,151,151,,,3440675044,2610927283,2684180140,5590878261,2486386,SRX5835156,SRS4761452,SRA880843,GEO,Zhejiang University,2,0.0,0.89661,0.0,0.03373,1.0,0.85821,,0.55774,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Fin,Surface Structure 52192,SRR9058955,SRX5835155,SRS4761451,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain8,GSM3768152,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain8,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768152,GSM3768152: Brain8; Danio rerio; RNA Seq,GSM3768152,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768152,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain8.bam,bam,61169120100.0,203897067.0,GSM3768152 r1,0:150 1:150,A:14774579191;C:10703170613;G:10764666983;T:24920342647;N:6360666,150,150,,,14774579191,10703170613,10764666983,24920342647,6360666,SRX5835155,SRS4761451,SRA880843,GEO,Zhejiang University,2,0.0,0.83877,0.0,0.06329,1.0,0.80486,,0.5111,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous System 52193,SRR9058954,SRX5835154,SRS4761450,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain6,GSM3768151,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain6,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768151,GSM3768151: Brain6; Danio rerio; RNA Seq,GSM3768151,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768151,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain6.bam,bam,23474213568.0,77729184.0,GSM3768151 r1,0:151 1:151,A:6103668811;C:3681973034;G:3710573267;T:9972513840;N:5484616,151,151,,,6103668811,3681973034,3710573267,9972513840,5484616,SRX5835154,SRS4761450,SRA880843,GEO,Zhejiang University,2,0.0,0.73533,0.0,0.06859,1.0,0.81726,,0.54249,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous System 52194,SRR9058953,SRX5835153,SRS4761449,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain5,GSM3768150,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain5,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768150,GSM3768150: Brain5; Danio rerio; RNA Seq,GSM3768150,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768150,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain5.bam,bam,22747830786.0,75323943.0,GSM3768150 r1,0:151 1:151,A:5518315065;C:4134426167;G:4150562230;T:8940682593;N:3844731,151,151,,,5518315065,4134426167,4150562230,8940682593,3844731,SRX5835153,SRS4761449,SRA880843,GEO,Zhejiang University,2,3e-05,0.9046,0.0,0.06433,0.99997,0.81377,1.0,0.62022,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous System 52195,SRR9058952,SRX5835152,SRS4761448,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain4,GSM3768149,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain4,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768149,GSM3768149: Brain4; Danio rerio; RNA Seq,GSM3768149,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768149,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain4.bam,bam,18433488000.0,61444960.0,GSM3768149 r1,0:150 1:150,A:4713818810;C:3042642974;G:3089017515;T:7586438228;N:1570473,150,150,,,4713818810,3042642974,3089017515,7586438228,1570473,SRX5835152,SRS4761448,SRA880843,GEO,Zhejiang University,2,2e-05,0.75385,0.0,0.06238,0.99997,0.78421,1.0,0.61521,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous System 52196,SRR9058951,SRX5835151,SRS4761447,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain2,GSM3768148,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain2,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768148,GSM3768148: Brain2; Danio rerio; RNA Seq,GSM3768148,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain2.bam,bam,11152563000.0,37175210.0,GSM3768148 r1,0:150 1:150,A:2999070684;C:1905797014;G:1888221389;T:4358535643;N:938270,150,150,,,2999070684,1905797014,1888221389,4358535643,938270,SRX5835151,SRS4761447,SRA880843,GEO,Zhejiang University,2,0.0,0.66661,0.0,0.03044,1.0,0.86427,,0.53019,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous System 52197,SRR9058950,SRX5835150,SRS4761446,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Brain1,GSM3768147,,source name:brain|strain:Tubingen|genotype/variation:wild type|tissue:brain,Brain1,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.,brain,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:brain,GSM3768147,GSM3768147: Brain1; Danio rerio; RNA Seq,GSM3768147,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768147,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Brain1.bam,bam,18455247000.0,61517490.0,GSM3768147 r1,0:150 1:150,A:5007204184;C:3213029200;G:3200729426;T:7030600172;N:3684018,150,150,,,5007204184,3213029200,3200729426,7030600172,3684018,SRX5835150,SRS4761446,SRA880843,GEO,Zhejiang University,2,3e-05,0.74031,0.0,0.13299,0.99997,0.82686,1.0,0.62886,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Brain,Nervous 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.,,pubmed:34660600,,Testis5,GSM3740961,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:testis,GSM3740961,GSM3740961: Testis5; Danio rerio; RNA Seq,GSM3740961,,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,,SRP194254,,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,,,6309984521,4265951177,4463773513,10013679424,67022705,SRX5770476,SRS4704585,SRA880843,GEO,Zhejiang University,2,0.0,0.73589,0.0,0.05677,1.0,0.76852,,0.48176,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Gonad,Reproductive System 52199,SRR8991407,SRX5770475,SRS4704584,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder1,GSM3740960,,source name:swim bladder|strain:Tubingen|genotype:wild type|tissue:swim bladder,Swim Bladder1,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.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:swim bladder,GSM3740960,GSM3740960: SwimmingBladder1; Danio rerio; RNA Seq,GSM3740960,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740960,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,SwimmingBladder1.bam,bam,35046550662.0,116048181.0,GSM3740960 r1,0:151 1:151,A:8395527831;C:6153137560;G:6277460016;T:14213583474;N:6841781,151,151,,,8395527831,6153137560,6277460016,14213583474,6841781,SRX5770475,SRS4704584,SRA880843,GEO,Zhejiang University,2,0.0,0.82455,0.0,0.03727,1.0,0.85423,,0.53813,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Swim Bladder,Swim Bladder 52200,SRR8991406,SRX5770474,SRS4704583,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Spleen3,GSM3740959,,source name:spleen|strain:Tubingen|genotype:wild type|tissue:spleen,Spleen3,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.,spleen,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:spleen,GSM3740959,GSM3740959: Spleen3; Danio rerio; RNA Seq,GSM3740959,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740959,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Spleen3.bam,bam,29617062386.0,98069743.0,GSM3740959 r1,0:151 1:151,A:7464139749;C:4972084318;G:5132144813;T:11970808438;N:77885068,151,151,,,7464139749,4972084318,5132144813,11970808438,77885068,SRX5770474,SRS4704583,SRA880843,GEO,Zhejiang University,2,0.0,0.7261,0.0,0.03774,1.0,0.86275,,0.5339,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Spleen,Hematopoietic System 52201,SRR8991405,SRX5770473,SRS4704582,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin4,GSM3740958,,source name:skin|strain:Tubingen|genotype:wild type|tissue:skin,Skin4,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.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:skin,GSM3740958,GSM3740958: Skin4; Danio rerio; RNA Seq,GSM3740958,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740958,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Skin4.bam,bam,33628232728.0,111351764.0,GSM3740958 r1,0:151 1:151,A:8460681247;C:5738320863;G:5953293918;T:13386336300;N:89600400,151,151,,,8460681247,5738320863,5953293918,13386336300,89600400,SRX5770473,SRS4704582,SRA880843,GEO,Zhejiang University,2,0.0,0.73034,0.0,0.03701,1.0,0.80454,,0.53563,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Skin,Surface Structure 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.,,pubmed:34660600,,Ovary3,GSM3740957,,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,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:ovary,GSM3740957,GSM3740957: Ovary3; Danio rerio; RNA Seq,GSM3740957,,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,,SRP194254,,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,,,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,,China,2019-04-30,Undetermined,Multi-stage,Gonad,Reproductive System 52203,SRR8991402,SRX5770470,SRS4704578,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Liver5,GSM3740955,,source name:liver|strain:Tubingen|genotype:wild type|tissue:liver,Liver5,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.,liver,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:liver,GSM3740955,GSM3740955: Liver5; Danio rerio; RNA Seq,GSM3740955,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Liver5.bam,bam,15710506288.0,52021544.0,GSM3740955 r1,0:151 1:151,A:3835047667;C:2793719034;G:2869155077;T:6209011033;N:3573477,151,151,,,3835047667,2793719034,2869155077,6209011033,3573477,SRX5770470,SRS4704578,SRA880843,GEO,Zhejiang University,2,0.0,0.85127,0.0,0.0145,1.0,0.90757,,0.53481,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Liver,Liver and Biliary System 52204,SRR8991401,SRX5770469,SRS4704579,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Kidney3,GSM3740954,,source name:kidney|strain:Tubingen|genotype:wild type|tissue:kidney,Kidney3,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.,kidney,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:kidney,GSM3740954,GSM3740954: Kidney3; Danio rerio; RNA Seq,GSM3740954,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740954,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Kidney3.bam,bam,47181267324.0,156229362.0,GSM3740954 r1,0:151 1:151,A:11942883398;C:7663399672;G:7892086087;T:19671671186;N:11226981,151,151,,,11942883398,7663399672,7892086087,19671671186,11226981,SRX5770469,SRS4704579,SRA880843,GEO,Zhejiang University,2,0.0,0.74871,0.0,0.03049,1.0,0.8658,,0.55011,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Kidney,Renal System 52205,SRR8991400,SRX5770468,SRS4704577,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Intestine5,GSM3740953,,source name:intestinePancreas|strain:Tubingen|genotype:wild type|tissue:intestinePancreas,Intestine5,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.,intestinePancreas,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:intestinePancreas,GSM3740953,GSM3740953: Intestine5; Danio rerio; RNA Seq,GSM3740953,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740953,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Intestine5.bam,bam,29368374144.0,97246272.0,GSM3740953 r1,0:151 1:151,A:7001017270;C:5160378687;G:5304225209;T:11829585834;N:73167144,151,151,,,7001017270,5160378687,5304225209,11829585834,73167144,SRX5770468,SRS4704577,SRA880843,GEO,Zhejiang University,2,0.0,0.76743,0.0,0.03069,1.0,0.88085,,0.51474,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Multi-tissue,Multi-system 52206,SRR8991399,SRX5770467,SRS4704576,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Heart5,GSM3740952,,source name:heart|strain:Tubingen|genotype:wild type|tissue:heart,Heart5,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.,heart,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:heart,GSM3740952,GSM3740952: Heart5; Danio rerio; RNA Seq,GSM3740952,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Heart5.bam,bam,43163633400.0,143878778.0,GSM3740952 r1,0:150 1:150,A:9349719585;C:8099097553;G:8061219131;T:17651447621;N:2149510,150,150,,,9349719585,8099097553,8061219131,17651447621,2149510,SRX5770467,SRS4704576,SRA880843,GEO,Zhejiang University,2,0.0,0.78756,0.0,0.01363,1.0,0.8994,,0.4146,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Heart,Cardiovascular System 52207,SRR8991397,SRX5770465,SRS4704574,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Eye2,GSM3740950,,source name:eye|strain:Tubingen|genotype:wild type|tissue:eye,Eye2,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.,eye,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:eye,GSM3740950,GSM3740950: Eye2; Danio rerio; RNA Seq,GSM3740950,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740950,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Eye2.bam,bam,37560825992.0,124373596.0,GSM3740950 r1,0:151 1:151,A:9124157397;C:6448456288;G:6525562883;T:15454078654;N:8570770,151,151,,,9124157397,6448456288,6525562883,15454078654,8570770,SRX5770465,SRS4704574,SRA880843,GEO,Zhejiang University,2,0.0,0.79235,0.0,0.0383,1.0,0.84981,,0.57745,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Eye,Sensory System 52208,SRR8991396,SRX5770464,SRS4704573,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,CaudalFin2,GSM3740949,,source name:caudal fin|strain:Tubingen|genotype:wild type|tissue:caudal fin,CaudalFin2,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.,caudal fin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:caudal fin,GSM3740949,GSM3740949: CaudalFin2; Danio rerio; RNA Seq,GSM3740949,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,CaudalFin2.bam,bam,34657911996.0,114761298.0,GSM3740949 r1,0:151 1:151,A:8439354130;C:5842860159;G:6009391550;T:14359478869;N:6827288,151,151,,,8439354130,5842860159,6009391550,14359478869,6827288,SRX5770464,SRS4704573,SRA880843,GEO,Zhejiang University,2,2e-05,0.79468,0.0,0.03917,0.99997,0.86393,0.0,0.58978,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Fin,Surface Structure