metadata: run_metadata: 55 rows where devstage_curation = "Undetermined" and technology = "microwellseq"

55 rows where devstage_curation = "Undetermined" and technology = "microwellseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
52150	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;