metadata: run_metadata: 765 rows where experiment.library_selection = "cDNA", technology = "microwellseq" and tissue_curation

765 rows where experiment.library_selection = "cDNA", technology = "microwellseq" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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
52169	52169	SRR10902878	SRX7571048	SRS6006649	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	72hpf 2	GSM4274624	source name:embryo\|strain:Tubingen\|tissue:embryo\|genotype:wild type	72hpf 2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	embryo	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:embryo\|genotype:wild type	GSM4274624	GSM4274624: 72hpf 2; Danio rerio; RNA Seq	GSM4274624	1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274624	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:GRCz10\|intentional duplicate	72hpf2.bam	bam	44540357958.0	147484629.0	GSM4274624 r1	0:151 1:151	A:11658483828;C:7854882099;G:7912135327;T:17103979590;N:10877114	151	151	11658483828	7854882099	7912135327	17103979590	10877114	SRX7571048	SRS6006649	SRA880843	GEO	Zhejiang University	2	0.0	0.70491	0.0	0.03368	1.0	0.81903		0.50131	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	Larval	Larval	Embryo Imprecise	All anatomical structures
52170	52170	SRR10902877	SRX7571047	SRS6006648	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	72hpf 1	GSM4274623	source name:embryo\|strain:Tubingen\|tissue:embryo\|genotype:wild type	72hpf 1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	embryo	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:embryo\|genotype:wild type	GSM4274623	GSM4274623: 72hpf 1; Danio rerio; RNA Seq	GSM4274623	1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274623	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:GRCz10\|intentional duplicate	72hpf1.bam	bam	10980000636.0	36357618.0	GSM4274623 r1	0:151 1:151	A:2869082796;C:1850640633;G:1873838761;T:4383874336;N:2564110	151	151	2869082796	1850640633	1873838761	4383874336	2564110	SRX7571047	SRS6006648	SRA880843	GEO	Zhejiang University	2	0.0	0.7282	0.0	0.02753	1.0	0.81716		0.47137	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	Larval	Larval	Embryo Imprecise	All anatomical structures
52171	52171	SRR10902876	SRX7571046	SRS6006647	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	24hpf 2	GSM4274622	source name:embryo\|strain:Tubingen\|tissue:embryo\|genotype:wild type	24hpf 2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	embryo	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:embryo\|genotype:wild type	GSM4274622	GSM4274622: 24hpf 2; Danio rerio; RNA Seq	GSM4274622	1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274622	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:GRCz10\|intentional duplicate	24hpf2.bam	bam	30695841720.0	101641860.0	GSM4274622 r1	0:151 1:151	A:8070725571;C:5211775632;G:5264888732;T:12140996276;N:7455509	151	151	8070725571	5211775632	5264888732	12140996276	7455509	SRX7571046	SRS6006647	SRA880843	GEO	Zhejiang University	2	2e-05	0.70368	0.0	0.01983	0.99997	0.84774	1.0	0.49229	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	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
52172	52172	SRR10902875	SRX7571045	SRS6006646	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	24hpf 1	GSM4274621	source name:embryo\|strain:Tubingen\|tissue:embryo\|genotype:wild type	24hpf 1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	embryo	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	strain:Tubingen\|tissue:embryo\|genotype:wild type	GSM4274621	GSM4274621: 24hpf 1; Danio rerio; RNA Seq	GSM4274621	1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274621	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:GRCz10\|intentional duplicate	24hpf1.bam	bam	36227583572.0	119958886.0	GSM4274621 r1	0:151 1:151	A:9526054168;C:6077203407;G:6186063574;T:14428929871;N:9332552	151	151	9526054168	6077203407	6186063574	14428929871	9332552	SRX7571045	SRS6006646	SRA880843	GEO	Zhejiang University	2	0.0	0.68951	0.0	0.01901	1.0	0.85173		0.47896	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	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
64506	64506	SRR17299063	SRX13476323	SRS11373166	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL58	GSM5746868	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL58	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746868	GSM5746868: Microwell seq datasets of Zebrafish 24hpf COL58; Danio rerio; RNA Seq	GSM5746868	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL58.bam	bam	91823975304.0	527723996.0	GSM5746868 r1	0:24 1:150	A:27162173122;C:19911517883;G:21018214314;T:23663599459;N:68470526	24	150	27162173122	19911517883	21018214314	23663599459	68470526	SRX13476323	SRS11373166	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00273	0.74807	0.00242	0.067	0.99949	0.84889	0.32	0.62031	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64507	64507	SRR17299062	SRX13476322	SRS11373165	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL57	GSM5746867	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL57	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746867	GSM5746867: Microwell seq datasets of Zebrafish 24hpf COL57; Danio rerio; RNA Seq	GSM5746867	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL57.bam	bam	83668974276.0	480856174.0	GSM5746867 r1	0:24 1:150	A:24589284117;C:18203396283;G:19071978317;T:21739883658;N:64431901	24	150	24589284117	18203396283	19071978317	21739883658	64431901	SRX13476322	SRS11373165	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00288	0.75168	0.00269	0.07335	0.99969	0.84419	0.6	0.6312	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64508	64508	SRR17299061	SRX13476321	SRS11373164	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL56	GSM5746866	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL56	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746866	GSM5746866: Microwell seq datasets of Zebrafish 24hpf COL56; Danio rerio; RNA Seq	GSM5746866	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL56.bam	bam	86257073418.0	495730307.0	GSM5746866 r1	0:24 1:150	A:25447223471;C:18668491192;G:19647110520;T:22426583347;N:67664888	24	150	25447223471	18668491192	19647110520	22426583347	67664888	SRX13476321	SRS11373164	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00275	0.73434	0.00255	0.07548	0.99967	0.84325	0.4375	0.5398	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64509	64509	SRR17299060	SRX13476320	SRS11373163	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL55	GSM5746865	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL55	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746865	GSM5746865: Microwell seq datasets of Zebrafish 24hpf COL55; Danio rerio; RNA Seq	GSM5746865	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL55.bam	bam	90331122120.0	519144380.0	GSM5746865 r1	0:24 1:150	A:26895594483;C:19418243460;G:20453276913;T:23498626121;N:65381143	24	150	26895594483	19418243460	20453276913	23498626121	65381143	SRX13476320	SRS11373163	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00295	0.73613	0.00277	0.07262	0.99971	0.83926	0.66666	0.56101	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64510	64510	SRR17299059	SRX13476319	SRS11373162	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL53	GSM5746864	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL53	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746864	GSM5746864: Microwell seq datasets of Zebrafish 24hpf COL53; Danio rerio; RNA Seq	GSM5746864	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL53.bam	bam	89040837126.0	511728949.0	GSM5746864 r1	0:24 1:150	A:26403646377;C:19129690981;G:20273444200;T:23171059435;N:62996133	24	150	26403646377	19129690981	20273444200	23171059435	62996133	SRX13476319	SRS11373162	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00256	0.73401	0.00242	0.07541	0.99977	0.83731	0.36363	0.56119	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64511	64511	SRR17299058	SRX13476318	SRS11373161	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL52	GSM5746863	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL52	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746863	GSM5746863: Microwell seq datasets of Zebrafish 24hpf COL52; Danio rerio; RNA Seq	GSM5746863	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL52.bam	bam	92071528062.0	529146713.0	GSM5746863 r1	0:24 1:150	A:27250499787;C:19863195558;G:21006813218;T:23884436340;N:66583159	24	150	27250499787	19863195558	21006813218	23884436340	66583159	SRX13476318	SRS11373161	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00303	0.73044	0.00285	0.07319	0.99969	0.84118	0.6	0.55998	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64512	64512	SRR17299057	SRX13476317	SRS11373160	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL51	GSM5746862	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL51	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746862	GSM5746862: Microwell seq datasets of Zebrafish 24hpf COL51; Danio rerio; RNA Seq	GSM5746862	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL51.bam	bam	89393336592.0	513754808.0	GSM5746862 r1	0:24 1:150	A:26357157407;C:19229237017;G:20353675917;T:23391840285;N:61425966	24	150	26357157407	19229237017	20353675917	23391840285	61425966	SRX13476317	SRS11373160	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00318	0.74297	0.003	0.07874	0.99969	0.83481	0.6	0.58428	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64513	64513	SRR17299056	SRX13476316	SRS11373159	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL50	GSM5746861	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL50	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:24 hours\|tissue:whole organism	GSM5746861	GSM5746861: Microwell seq datasets of Zebrafish 24hpf COL50; Danio rerio; RNA Seq	GSM5746861	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL50.bam	bam	93180912216.0	535522484.0	GSM5746861 r1	0:24 1:150	A:27511179288;C:19943495783;G:21163186103;T:24482014463;N:81036579	24	150	27511179288	19943495783	21163186103	24482014463	81036579	SRX13476316	SRS11373159	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00287	0.73081	0.00269	0.08165	0.99969	0.83469	0.53333	0.56313	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64515	64515	SRR17137061	SRX13321491	SRS11229252	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL103	GSM5718327	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL103	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718327	GSM5718327: Microwell seq datasets of Zebrafish 72hpf COL103; Danio rerio; RNA Seq	GSM5718327	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL103.bam	bam	97437769842.0	559987183.0	GSM5718327 r1	0:24 1:150	A:28425257606;C:21026057575;G:22210354179;T:25724166722;N:51933760	24	150	28425257606	21026057575	22210354179	25724166722	51933760	SRX13321491	SRS11229252	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00232	0.76296	0.00214	0.09247	0.99975	0.7963	0.58333	0.50975	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64516	64516	SRR17137060	SRX13321490	SRS11229251	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL102	GSM5718326	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL102	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718326	GSM5718326: Microwell seq datasets of Zebrafish 72hpf COL102; Danio rerio; RNA Seq	GSM5718326	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL102.bam	bam	99647119878.0	572684597.0	GSM5718326 r1	0:24 1:150	A:29163675513;C:21410312143;G:22841561495;T:26179135838;N:52434889	24	150	29163675513	21410312143	22841561495	26179135838	52434889	SRX13321490	SRS11229251	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00211	0.75462	0.00197	0.08783	0.99979	0.79614	0.6	0.48777	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64517	64517	SRR17137059	SRX13321489	SRS11229250	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL101	GSM5718325	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL101	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718325	GSM5718325: Microwell seq datasets of Zebrafish 72hpf COL101; Danio rerio; RNA Seq	GSM5718325	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL101.bam	bam	103850532360.0	596842140.0	GSM5718325 r1	0:24 1:150	A:30253504994;C:22208170461;G:23486370057;T:27846281411;N:56205437	24	150	30253504994	22208170461	23486370057	27846281411	56205437	SRX13321489	SRS11229250	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00248	0.76955	0.00238	0.09242	0.99985	0.78549	0.0	0.48332	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64518	64518	SRR17137058	SRX13321488	SRS11229249	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL100	GSM5718324	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL100	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718324	GSM5718324: Microwell seq datasets of Zebrafish 72hpf COL100; Danio rerio; RNA Seq	GSM5718324	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL100.bam	bam	79732033224.0	458230076.0	GSM5718324 r1	0:24 1:150	A:23142121477;C:17273443279;G:18152994838;T:21124595570;N:38878060	24	150	23142121477	17273443279	18152994838	21124595570	38878060	SRX13321488	SRS11229249	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0019	0.78954	0.00176	0.1	0.99977	0.79302	0.45454	0.53183	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64519	64519	SRR17137057	SRX13321487	SRS11229248	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL99	GSM5718323	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL99	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718323	GSM5718323: Microwell seq datasets of Zebrafish 72hpf COL99; Danio rerio; RNA Seq	GSM5718323	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL99.bam	bam	57905355774.0	332789401.0	GSM5718323 r1	0:24 1:150	A:16732054497;C:12484254815;G:13099812159;T:15561038953;N:28195350	24	150	16732054497	12484254815	13099812159	15561038953	28195350	SRX13321487	SRS11229248	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0023	0.79516	0.00213	0.10777	0.99977	0.79413	0.5	0.52425	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64520	64520	SRR17137056	SRX13321486	SRS11229247	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL98	GSM5718322	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL98	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718322	GSM5718322: Microwell seq datasets of Zebrafish 72hpf COL98; Danio rerio; RNA Seq	GSM5718322	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL98.bam	bam	133922399388.0	769668962.0	GSM5718322 r1	0:24 1:150	A:39157671234;C:28685783001;G:30222645162;T:35787052837;N:69247154	24	150	39157671234	28685783001	30222645162	35787052837	69247154	SRX13321486	SRS11229247	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00205	0.77779	0.00189	0.10045	0.99977	0.7903	0.36363	0.52076	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64521	64521	SRR17137055	SRX13321485	SRS11229246	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL97	GSM5718321	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL97	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5718321	GSM5718321: Microwell seq datasets of Zebrafish 72hpf COL97; Danio rerio; RNA Seq	GSM5718321	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL97.bam	bam	102882979782.0	591281493.0	GSM5718321 r1	0:24 1:150	A:30066107926;C:21991309044;G:23041144876;T:27728508333;N:55909603	24	150	30066107926	21991309044	23041144876	27728508333	55909603	SRX13321485	SRS11229246	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00231	0.78387	0.00216	0.09479	0.99977	0.78638	0.63636	0.48401	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64522	64522	SRR17075126	SRX13263481	SRS11185248	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL92	GSM5709061	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL92	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709061	GSM5709061: Micorwell seq datasets of Zebrafish 72hpf COL92; Danio rerio; RNA Seq	GSM5709061	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL92.bam	bam	93305697882.0	536239643.0	GSM5709061 r1	0:24 1:150	A:27107741517;C:19830183542;G:20994123402;T:25327971257;N:45678164	24	150	27107741517	19830183542	20994123402	25327971257	45678164	SRX13263481	SRS11185248	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00194	0.78236	0.00179	0.10164	0.99975	0.78618	0.75	0.48898	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64523	64523	SRR17075125	SRX13263480	SRS11185247	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL91	GSM5709060	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL91	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709060	GSM5709060: Micorwell seq datasets of Zebrafish 72hpf COL91; Danio rerio; RNA Seq	GSM5709060	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL91.bam	bam	96227810904.0	553033396.0	GSM5709060 r1	0:24 1:150	A:27923073482;C:20564137902;G:21719882675;T:25970776374;N:49940471	24	150	27923073482	20564137902	21719882675	25970776374	49940471	SRX13263480	SRS11185247	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0019	0.78115	0.00184	0.10758	0.99989	0.78725	0.4	0.49305	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64524	64524	SRR17075124	SRX13263479	SRS11185246	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL90	GSM5709059	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL90	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709059	GSM5709059: Micorwell seq datasets of Zebrafish 72hpf COL90; Danio rerio; RNA Seq	GSM5709059	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL90.bam	bam	101004540858.0	580485867.0	GSM5709059 r1	0:24 1:150	A:29424345909;C:21610893920;G:22734702528;T:27180463498;N:54135003	24	150	29424345909	21610893920	22734702528	27180463498	54135003	SRX13263479	SRS11185246	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00188	0.78353	0.00176	0.10575	0.99981	0.78699	0.55555	0.50829	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64525	64525	SRR17075123	SRX13263478	SRS11185245	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL89	GSM5709058	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL89	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709058	GSM5709058: Micorwell seq datasets of Zebrafish 72hpf COL89; Danio rerio; RNA Seq	GSM5709058	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL89.bam	bam	103228879080.0	593269420.0	GSM5709058 r1	0:24 1:150	A:30122538038;C:21933106979;G:23172314020;T:27949125385;N:51794658	24	150	30122538038	21933106979	23172314020	27949125385	51794658	SRX13263478	SRS11185245	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00229	0.78058	0.00208	0.11813	0.99967	0.78642	0.4375	0.51666	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64526	64526	SRR17075130	SRX13263477	SRS11185244	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL96	GSM5709065	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL96	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709065	GSM5709065: Micorwell seq datasets of Zebrafish 72hpf COL96; Danio rerio; RNA Seq	GSM5709065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL96.bam	bam	72161390838.0	414720637.0	GSM5709065 r1	0:24 1:150	A:20858972054;C:15631755598;G:16378791674;T:19256108785;N:35762727	24	150	20858972054	15631755598	16378791674	19256108785	35762727	SRX13263477	SRS11185244	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0024	0.78585	0.00221	0.10389	0.99971	0.79099	0.64285	0.51929	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64527	64527	SRR17075129	SRX13263476	SRS11185243	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL95	GSM5709064	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL95	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709064	GSM5709064: Micorwell seq datasets of Zebrafish 72hpf COL95; Danio rerio; RNA Seq	GSM5709064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL95.bam	bam	116725350900.0	670835350.0	GSM5709064 r1	0:24 1:150	A:33766055210;C:25258192198;G:26422558801;T:31219012086;N:59532605	24	150	33766055210	25258192198	26422558801	31219012086	59532605	SRX13263476	SRS11185243	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00223	0.78242	0.00205	0.10222	0.99973	0.7948	0.76923	0.51107	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64528	64528	SRR17075128	SRX13263475	SRS11185241	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL94	GSM5709063	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL94	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709063	GSM5709063: Micorwell seq datasets of Zebrafish 72hpf COL94; Danio rerio; RNA Seq	GSM5709063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL94.bam	bam	115204393758.0	662094217.0	GSM5709063 r1	0:24 1:150	A:33385976074;C:24728619684;G:25999313932;T:31027995525;N:62488543	24	150	33385976074	24728619684	25999313932	31027995525	62488543	SRX13263475	SRS11185241	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00227	0.78471	0.00206	0.10458	0.99967	0.78591	0.4375	0.50275	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64529	64529	SRR17075127	SRX13263474	SRS11185242	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL93	GSM5709062	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL93	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5709062	GSM5709062: Micorwell seq datasets of Zebrafish 72hpf COL93; Danio rerio; RNA Seq	GSM5709062	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL93.bam	bam	109890007632.0	631551768.0	GSM5709062 r1	0:24 1:150	A:31784495967;C:23590735781;G:24835459995;T:29625393694;N:53922195	24	150	31784495967	23590735781	24835459995	29625393694	53922195	SRX13263474	SRS11185242	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00221	0.77545	0.002	0.11238	0.99969	0.78879	0.4375	0.50979	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64530	64530	SRR17010806	SRX13200959	SRS11127611	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL88	GSM5699934	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL88	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699934	GSM5699934: Micorwell seq datasets of Zebrafish 72hpf COL88; Danio rerio; RNA Seq	GSM5699934	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL88.bam	bam	105325546890.0	605319235.0	GSM5699934 r1	0:24 1:150	A:30618141170;C:22639431941;G:23832910711;T:28175599693;N:59463375	24	150	30618141170	22639431941	23832910711	28175599693	59463375	SRX13200959	SRS11127611	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00204	0.77653	0.00184	0.1038	0.99969	0.78896	0.4	0.49664	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64531	64531	SRR17010805	SRX13200958	SRS11127610	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL87	GSM5699933	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL87	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699933	GSM5699933: Micorwell seq datasets of Zebrafish 72hpf COL87; Danio rerio; RNA Seq	GSM5699933	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL87.bam	bam	104410657848.0	600061252.0	GSM5699933 r1	0:24 1:150	A:30448105235;C:22372529466;G:23651054417;T:27884763811;N:54204919	24	150	30448105235	22372529466	23651054417	27884763811	54204919	SRX13200958	SRS11127610	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00239	0.76912	0.00221	0.11084	0.99971	0.78847	0.5	0.51741	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64532	64532	SRR17010804	SRX13200957	SRS11127609	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL86	GSM5699932	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL86	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699932	GSM5699932: Micorwell seq datasets of Zebrafish 72hpf COL86; Danio rerio; RNA Seq	GSM5699932	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL86.bam	bam	85539017526.0	491603549.0	GSM5699932 r1	0:24 1:150	A:24891444353;C:18382714837;G:19465935988;T:22755762595;N:43159753	24	150	24891444353	18382714837	19465935988	22755762595	43159753	SRX13200957	SRS11127609	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00186	0.7737	0.00168	0.10503	0.99973	0.78553	0.35714	0.52806	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64533	64533	SRR17010803	SRX13200956	SRS11127608	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL85	GSM5699931	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL85	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699931	GSM5699931: Micorwell seq datasets of Zebrafish 72hpf COL85; Danio rerio; RNA Seq	GSM5699931	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL85.bam	bam	96579499182.0	555054593.0	GSM5699931 r1	0:24 1:150	A:28258999810;C:20566647022;G:21776511096;T:25928948228;N:48393026	24	150	28258999810	20566647022	21776511096	25928948228	48393026	SRX13200956	SRS11127608	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00215	0.77075	0.00203	0.09684	0.99981	0.78348	0.44444	0.50291	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64534	64534	SRR17010802	SRX13200955	SRS11127607	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL84	GSM5699930	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL84	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699930	GSM5699930: Micorwell seq datasets of Zebrafish 72hpf COL84; Danio rerio; RNA Seq	GSM5699930	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL84.bam	bam	95402087292.0	548287858.0	GSM5699930 r1	0:24 1:150	A:27920812951;C:20371734068;G:21595614980;T:25463535654;N:50389639	24	150	27920812951	20371734068	21595614980	25463535654	50389639	SRX13200955	SRS11127607	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00199	0.76291	0.00186	0.09597	0.99981	0.79001	0.3	0.50069	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64535	64535	SRR17010801	SRX13200954	SRS11127606	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL83	GSM5699929	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL83	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699929	GSM5699929: Micorwell seq datasets of Zebrafish 72hpf COL83; Danio rerio; RNA Seq	GSM5699929	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL83.bam	bam	94589605254.0	543618421.0	GSM5699929 r1	0:24 1:150	A:27596905697;C:20243328527;G:21378738112;T:25321573995;N:49058923	24	150	27596905697	20243328527	21378738112	25321573995	49058923	SRX13200954	SRS11127606	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00216	0.77625	0.00202	0.09982	0.99979	0.78831	0.36363	0.51012	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64536	64536	SRR17010800	SRX13200953	SRS11127605	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL82	GSM5699928	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL82	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699928	GSM5699928: Micorwell seq datasets of Zebrafish 72hpf COL82; Danio rerio; RNA Seq	GSM5699928	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL82.bam	bam	89062661598.0	511854377.0	GSM5699928 r1	0:24 1:150	A:26102790989;C:19094974289;G:20282271482;T:23541508213;N:41116625	24	150	26102790989	19094974289	20282271482	23541508213	41116625	SRX13200953	SRS11127605	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00227	0.76728	0.00206	0.10248	0.99969	0.79196	0.29411	0.53203	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64537	64537	SRR17010799	SRX13200952	SRS11127604	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL81	GSM5699927	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL81	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:72 hours\|tissue:whole organism	GSM5699927	GSM5699927: Micorwell seq datasets of Zebrafish 72hpf COL81; Danio rerio; RNA Seq	GSM5699927	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL81.bam	bam	97306386444.0	559232106.0	GSM5699927 r1	0:24 1:150	A:28504741466;C:20782464199;G:21987624297;T:25985173510;N:46382972	24	150	28504741466	20782464199	21987624297	25985173510	46382972	SRX13200952	SRS11127604	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00232	0.76473	0.00224	0.09727	0.99987	0.79153	0.66666	0.51198	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64538	64538	SRR14915030	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_1_1.fq.gz Zebrafish_3m_COL64_1_2.fq.gz	fastq fastq	3509355300.0	23395702.0	GSM5400025 r1	0:150 1:150	A:1033838372;C:621125453;G:637527732;T:1213662404;N:3201339	150	150	1033838372	621125453	637527732	1213662404	3201339	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.36321		0.02305		0.82554		0.50827		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64539	64539	SRR14915031	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_2_1.fq.gz Zebrafish_3m_COL64_2_2.fq.gz	fastq fastq	1665060900.0	11100406.0	GSM5400025 r2	0:150 1:150	A:462369470;C:317060096;G:327014453;T:557786784;N:830097	150	150	462369470	317060096	327014453	557786784	830097	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13839		0.00808		0.91569		0.53255		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64540	64540	SRR14915032	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_3_1.fq.gz Zebrafish_3m_COL64_3_2.fq.gz	fastq fastq	2150244600.0	14334964.0	GSM5400025 r3	0:150 1:150	A:601841098;C:403651653;G:418726941;T:723163387;N:2861521	150	150	601841098	403651653	418726941	723163387	2861521	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.14947		0.00856		0.91563		0.52901		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64541	64541	SRR14915033	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_4_1.fq.gz Zebrafish_3m_COL64_4_2.fq.gz	fastq fastq	2197416600.0	14649444.0	GSM5400025 r4	0:150 1:150	A:623049639;C:408736499;G:423211202;T:740201304;N:2217956	150	150	623049639	408736499	423211202	740201304	2217956	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.31503		0.01599		0.86805		0.52639		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64542	64542	SRR14915034	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_5_1.fq.gz Zebrafish_3m_COL64_5_2.fq.gz	fastq fastq	15591467400.0	103943116.0	GSM5400025 r5	0:150 1:150	A:4293072963;C:3172864759;G:3328412245;T:4775949229;N:21168204	150	150	4293072963	3172864759	3328412245	4775949229	21168204	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.42792		0.02171		0.85798		0.53122		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64543	64543	SRR14915035	SRX11229465	SRS9283357	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL64	GSM5400025	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL64	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400025	GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq	GSM5400025	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL64_6_1.fq.gz Zebrafish_3m_COL64_6_2.fq.gz	fastq fastq	12549507270.0	144247210.0	GSM5400025 r6	0:24 1:150	A:4029002995;C:2554410310;G:2623555177;T:3319223578;N:23315210	24	150	4029002995	2554410310	2623555177	3319223578	23315210	SRX11229465	SRS9283357	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.38859		0.01815		0.85269		0.5308		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64544	64544	SRR14915024	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_1_1.fq.gz Zebrafish_3m_COL63_1_2.fq.gz	fastq fastq	2055042600.0	13700284.0	GSM5400024 r1	0:150 1:150	A:611481772;C:368434834;G:377372486;T:695791152;N:1962356	150	150	611481772	368434834	377372486	695791152	1962356	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.34483		0.02058		0.82974		0.52413		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64545	64545	SRR14915025	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_2_1.fq.gz Zebrafish_3m_COL63_2_2.fq.gz	fastq fastq	160975800.0	1073172.0	GSM5400024 r2	0:150 1:150	A:44979062;C:31715522;G:32816505;T:51394061;N:70650	150	150	44979062	31715522	32816505	51394061	70650	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.14018		0.00811		0.91565		0.53293		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64546	64546	SRR14915026	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_3_1.fq.gz Zebrafish_3m_COL63_3_2.fq.gz	fastq fastq	948599100.0	6323994.0	GSM5400024 r3	0:150 1:150	A:270719772;C:179859378;G:186167273;T:310493229;N:1359448	150	150	270719772	179859378	186167273	310493229	1359448	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.15861		0.00833		0.90536		0.53615		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64547	64547	SRR14915027	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_4_1.fq.gz Zebrafish_3m_COL63_4_2.fq.gz	fastq fastq	1296727200.0	8644848.0	GSM5400024 r4	0:150 1:150	A:373182160;C:244740194;G:252531468;T:424978804;N:1294574	150	150	373182160	244740194	252531468	424978804	1294574	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.30429		0.0152		0.86466		0.53074		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64548	64548	SRR14915028	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_5_1.fq.gz Zebrafish_3m_COL63_5_2.fq.gz	fastq fastq	7785040500.0	51900270.0	GSM5400024 r5	0:150 1:150	A:2174090918;C:1597924965;G:1665177229;T:2337394238;N:10453150	150	150	2174090918	1597924965	1665177229	2337394238	10453150	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.41787		0.01939		0.85403		0.5287		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64549	64549	SRR14915029	SRX11229464	SRS9283356	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL63	GSM5400024	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL63	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400024	GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq	GSM5400024	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL63_6_1.fq.gz Zebrafish_3m_COL63_6_2.fq.gz	fastq fastq	5937968196.0	68252508.0	GSM5400024 r6	0:24 1:150	A:1934581537;C:1211880492;G:1231715977;T:1548193534;N:11596656	24	150	1934581537	1211880492	1231715977	1548193534	11596656	SRX11229464	SRS9283356	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.37443		0.0171		0.85352		0.52813		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64550	64550	SRR14915018	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_1_1.fq.gz Zebrafish_3m_COL62_1_2.fq.gz	fastq fastq	1789905600.0	11932704.0	GSM5400023 r1	0:150 1:150	A:537842325;C:316956626;G:324348756;T:609120570;N:1637323	150	150	537842325	316956626	324348756	609120570	1637323	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.33127		0.02101		0.84187		0.5271		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64551	64551	SRR14915019	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_2_1.fq.gz Zebrafish_3m_COL62_2_2.fq.gz	fastq fastq	1289058300.0	8593722.0	GSM5400023 r2	0:150 1:150	A:365275974;C:247054954;G:250766392;T:425210421;N:750559	150	150	365275974	247054954	250766392	425210421	750559	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.11204		0.00628		0.92967		0.53143		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64552	64552	SRR14915020	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_3_1.fq.gz Zebrafish_3m_COL62_3_2.fq.gz	fastq fastq	1468221600.0	9788144.0	GSM5400023 r3	0:150 1:150	A:422901616;C:273721436;G:280933485;T:488734495;N:1930568	150	150	422901616	273721436	280933485	488734495	1930568	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13434		0.00748		0.92383		0.53386		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64553	64553	SRR14915021	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_4_1.fq.gz Zebrafish_3m_COL62_4_2.fq.gz	fastq fastq	1551007800.0	10340052.0	GSM5400023 r4	0:150 1:150	A:450556375;C:286977972;G:294533181;T:517371969;N:1568303	150	150	450556375	286977972	294533181	517371969	1568303	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.27413		0.01353		0.88065		0.5239		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64554	64554	SRR14915022	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_5_1.fq.gz Zebrafish_3m_COL62_5_2.fq.gz	fastq fastq	8141951700.0	54279678.0	GSM5400023 r5	0:150 1:150	A:2279713850;C:1655964521;G:1727447219;T:2467915358;N:10910752	150	150	2279713850	1655964521	1727447219	2467915358	10910752	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.40205		0.02062		0.86571		0.53401		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64555	64555	SRR14915023	SRX11229463	SRS9283353	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL62	GSM5400023	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL62	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400023	GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq	GSM5400023	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL62_6_1.fq.gz Zebrafish_3m_COL62_6_2.fq.gz	fastq fastq	6366133998.0	73173954.0	GSM5400023 r6	0:24 1:150	A:2133593269;C:1284155615;G:1311954143;T:1624544767;N:11886204	24	150	2133593269	1284155615	1311954143	1624544767	11886204	SRX11229463	SRS9283353	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.3596		0.01726		0.86519		0.50248		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64556	64556	SRR14915012	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_1_1.fq.gz Zebrafish_3m_COL61_1_2.fq.gz	fastq fastq	4243314900.0	28288766.0	GSM5400022 r1	0:150 1:150	A:1245557842;C:757040428;G:775787197;T:1461026513;N:3902920	150	150	1245557842	757040428	775787197	1461026513	3902920	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.37049		0.02368		0.82613		0.52976		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64557	64557	SRR14915013	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_2_1.fq.gz Zebrafish_3m_COL61_2_2.fq.gz	fastq fastq	1240206900.0	8268046.0	GSM5400022 r2	0:150 1:150	A:342697940;C:238587916;G:245987086;T:412298823;N:635135	150	150	342697940	238587916	245987086	412298823	635135	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13399		0.008		0.9181		0.52385		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64558	64558	SRR14915014	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_3_1.fq.gz Zebrafish_3m_COL61_3_2.fq.gz	fastq fastq	1347541200.0	8983608.0	GSM5400022 r3	0:150 1:150	A:378035707;C:253070106;G:262848999;T:451676944;N:1909444	150	150	378035707	253070106	262848999	451676944	1909444	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.16482		0.00934		0.90414		0.54039		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64559	64559	SRR14915015	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_4_1.fq.gz Zebrafish_3m_COL61_4_2.fq.gz	fastq fastq	2103237600.0	14021584.0	GSM5400022 r4	0:150 1:150	A:595972315;C:392671732;G:407063253;T:705390065;N:2140235	150	150	595972315	392671732	407063253	705390065	2140235	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.32134		0.01649		0.86316		0.49587		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64560	64560	SRR14915016	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_5_1.fq.gz Zebrafish_3m_COL61_5_2.fq.gz	fastq fastq	19534617300.0	130230782.0	GSM5400022 r5	0:150 1:150	A:5361819748;C:3997534297;G:4189722611;T:5957688281;N:27852363	150	150	5361819748	3997534297	4189722611	5957688281	27852363	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.43627		0.02217		0.85693		0.53022		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64561	64561	SRR14915017	SRX11229462	SRS9283355	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL61	GSM5400022	source name:Zebrafish 3m sample3\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL61	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400022	GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq	GSM5400022	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL61_6_1.fq.gz Zebrafish_3m_COL61_6_2.fq.gz	fastq fastq	15060602538.0	173110374.0	GSM5400022 r6	0:24 1:150	A:4814003802;C:3077509029;G:3135215248;T:4005264504;N:28609955	24	150	4814003802	3077509029	3135215248	4005264504	28609955	SRX11229462	SRS9283355	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.39158		0.01982		0.85348		0.51089		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64562	64562	SRR14915286	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_1_1.fq.gz Zebrafish_3m_COL128_1_2.fq.gz	fastq fastq	3208770600.0	21391804.0	GSM5400069 r1	0:150 1:150	A:945845308;C:569438484;G:585368535;T:1105095075;N:3023198	150	150	945845308	569438484	585368535	1105095075	3023198	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.3414		0.02928		0.85021		0.51782		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64563	64563	SRR14915287	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_2_1.fq.gz Zebrafish_3m_COL128_2_2.fq.gz	fastq fastq	304801800.0	2032012.0	GSM5400069 r2	0:150 1:150	A:84325161;C:57825170;G:60519262;T:102006710;N:125497	150	150	84325161	57825170	60519262	102006710	125497	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.14941		0.01173		0.92151		0.54623		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64564	64564	SRR14915288	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_3_1.fq.gz Zebrafish_3m_COL128_3_2.fq.gz	fastq fastq	1191613200.0	7944088.0	GSM5400069 r3	0:150 1:150	A:334533793;C:224286886;G:233943665;T:397197115;N:1651741	150	150	334533793	224286886	233943665	397197115	1651741	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.15569		0.0115		0.9207		0.54743		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64565	64565	SRR14915289	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_4_1.fq.gz Zebrafish_3m_COL128_4_2.fq.gz	fastq fastq	1766814000.0	11778760.0	GSM5400069 r4	0:150 1:150	A:500417014;C:333000747;G:344717291;T:586926285;N:1752663	150	150	500417014	333000747	344717291	586926285	1752663	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.29677		0.01992		0.88645		0.54665		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64566	64566	SRR14915290	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_5_1.fq.gz Zebrafish_3m_COL128_5_2.fq.gz	fastq fastq	15144379800.0	100962532.0	GSM5400069 r5	0:150 1:150	A:4075035270;C:3166217509;G:3409509586;T:4473533042;N:20084393	150	150	4075035270	3166217509	3409509586	4473533042	20084393	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.37107		0.02472		0.88509		0.54349		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64567	64567	SRR14915291	SRX11229461	SRS9283354	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL128	GSM5400069	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL128	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400069	GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq	GSM5400069	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL128_6_1.fq.gz Zebrafish_3m_COL128_6_2.fq.gz	fastq fastq	11721521832.0	134730136.0	GSM5400069 r6	0:24 1:150	A:3640769264;C:2518212610;G:2406793302;T:3133328455;N:22418201	24	150	3640769264	2518212610	2406793302	3133328455	22418201	SRX11229461	SRS9283354	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.34007		0.02128		0.88032		0.54961		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64568	64568	SRR14915280	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_1_1.fq.gz Zebrafish_3m_COL127_1_2.fq.gz	fastq fastq	2746310400.0	18308736.0	GSM5400068 r1	0:150 1:150	A:806781242;C:487253172;G:500916690;T:948772411;N:2586885	150	150	806781242	487253172	500916690	948772411	2586885	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.36116		0.03633		0.84587		0.53626		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64569	64569	SRR14915281	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_2_1.fq.gz Zebrafish_3m_COL127_2_2.fq.gz	fastq fastq	1701404100.0	11342694.0	GSM5400068 r2	0:150 1:150	A:469834000;C:332532377;G:339422396;T:558600197;N:1015130	150	150	469834000	332532377	339422396	558600197	1015130	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.1265		0.01237		0.93152		0.53316		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64570	64570	SRR14915282	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_3_1.fq.gz Zebrafish_3m_COL127_3_2.fq.gz	fastq fastq	1339582500.0	8930550.0	GSM5400068 r3	0:150 1:150	A:374492185;C:255730803;G:264255158;T:443331862;N:1772492	150	150	374492185	255730803	264255158	443331862	1772492	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.15302		0.01389		0.9236		0.52455		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64571	64571	SRR14915283	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_4_1.fq.gz Zebrafish_3m_COL127_4_2.fq.gz	fastq fastq	1367540100.0	9116934.0	GSM5400068 r4	0:150 1:150	A:387379474;C:258496197;G:266901212;T:453386759;N:1376458	150	150	387379474	258496197	266901212	453386759	1376458	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.32389		0.02782		0.87913		0.53804		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64572	64572	SRR14915284	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_5_1.fq.gz Zebrafish_3m_COL127_5_2.fq.gz	fastq fastq	10892960400.0	72619736.0	GSM5400068 r5	0:150 1:150	A:3010970636;C:2227858579;G:2327578951;T:3312264759;N:14287475	150	150	3010970636	2227858579	2327578951	3312264759	14287475	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.41723		0.03455		0.87345		0.53603		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64573	64573	SRR14915285	SRX11229460	SRS9289443	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL127	GSM5400068	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL127	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400068	GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq	GSM5400068	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL127_6_1.fq.gz Zebrafish_3m_COL127_6_2.fq.gz	fastq fastq	8590523028.0	98741644.0	GSM5400068 r6	0:24 1:150	A:2744332263;C:1751755618;G:1790836239;T:2287153559;N:16445349	24	150	2744332263	1751755618	1790836239	2287153559	16445349	SRX11229460	SRS9289443	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.37598		0.02831		0.87028		0.53692		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64574	64574	SRR14915274	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_1_1.fq.gz Zebrafish_3m_COL126_1_2.fq.gz	fastq fastq	3367480500.0	22449870.0	GSM5400067 r1	0:150 1:150	A:988357060;C:594065773;G:612600123;T:1169171017;N:3286527	150	150	988357060	594065773	612600123	1169171017	3286527	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.36442		0.03788		0.83707		0.53153		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64575	64575	SRR14915275	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_2_1.fq.gz Zebrafish_3m_COL126_2_2.fq.gz	fastq fastq	2217890100.0	14785934.0	GSM5400067 r2	0:150 1:150	A:611233800;C:426890176;G:440427980;T:738097977;N:1240167	150	150	611233800	426890176	440427980	738097977	1240167	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13061		0.01274		0.92186		0.52329		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64576	64576	SRR14915276	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_3_1.fq.gz Zebrafish_3m_COL126_3_2.fq.gz	fastq fastq	2127274200.0	14181828.0	GSM5400067 r3	0:150 1:150	A:592506103;C:401844212;G:419018214;T:711110076;N:2795595	150	150	592506103	401844212	419018214	711110076	2795595	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.15085		0.01391		0.91912		0.50158		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64577	64577	SRR14915277	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_4_1.fq.gz Zebrafish_3m_COL126_4_2.fq.gz	fastq fastq	2170011000.0	14466740.0	GSM5400067 r4	0:150 1:150	A:612178252;C:405838172;G:422117791;T:727705097;N:2171688	150	150	612178252	405838172	422117791	727705097	2171688	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.31735		0.02846		0.87111		0.51932		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64578	64578	SRR14915278	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_5_2.fq.gz Zebrafish_3m_COL126_5_1.fq.gz	fastq fastq	12412172700.0	82747818.0	GSM5400067 r5	0:150 1:150	A:3428337367;C:2521025487;G:2650242372;T:3796533380;N:16034094	150	150	3428337367	2521025487	2650242372	3796533380	16034094	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.422		0.03542		0.8661		0.54056		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64579	64579	SRR14915279	SRX11229459	SRS9283351	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL126	GSM5400067	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL126	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400067	GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq	GSM5400067	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL126_6_1.fq.gz Zebrafish_3m_COL126_6_2.fq.gz	fastq fastq	10084544970.0	115914310.0	GSM5400067 r6	0:24 1:150	A:3246792678;C:2042678037;G:2092562882;T:2683662920;N:18848453	24	150	3246792678	2042678037	2092562882	2683662920	18848453	SRX11229459	SRS9283351	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.3807		0.03251		0.86726		0.53521		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64580	64580	SRR14915268	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_1_1.fq.gz Zebrafish_3m_COL125_1_2.fq.gz	fastq fastq	3535998000.0	23573320.0	GSM5400066 r1	0:150 1:150	A:1034469165;C:634010669;G:649729630;T:1214431364;N:3357172	150	150	1034469165	634010669	649729630	1214431364	3357172	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.34196		0.03294		0.84796		0.53906		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64581	64581	SRR14915269	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_2_1.fq.gz Zebrafish_3m_COL125_2_2.fq.gz	fastq fastq	2034814800.0	13565432.0	GSM5400066 r2	0:150 1:150	A:561299001;C:400914760;G:406578613;T:664823715;N:1198711	150	150	561299001	400914760	406578613	664823715	1198711	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.11368		0.01046		0.93576		0.5358		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64582	64582	SRR14915270	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_3_1.fq.gz Zebrafish_3m_COL125_3_2.fq.gz	fastq fastq	1715258700.0	11435058.0	GSM5400066 r3	0:150 1:150	A:478425920;C:330213303;G:338928699;T:565440723;N:2250055	150	150	478425920	330213303	338928699	565440723	2250055	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13635		0.01121		0.93095		0.51679		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64583	64583	SRR14915271	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_4_1.fq.gz Zebrafish_3m_COL125_4_2.fq.gz	fastq fastq	1715104500.0	11434030.0	GSM5400066 r4	0:150 1:150	A:484886997;C:327078444;G:334782640;T:566633787;N:1722632	150	150	484886997	327078444	334782640	566633787	1722632	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.2998		0.02457		0.88629		0.5217		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64584	64584	SRR14915272	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_5_2.fq.gz Zebrafish_3m_COL125_5_1.fq.gz	fastq fastq	15018441600.0	100122944.0	GSM5400066 r5	0:150 1:150	A:4129076288;C:3096636754;G:3227410655;T:4544987986;N:20329917	150	150	4129076288	3096636754	3227410655	4544987986	20329917	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.39068		0.03076		0.87982		0.53718		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64585	64585	SRR14915273	SRX11229458	SRS9283350	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL125	GSM5400066	source name:Zebrafish 3m sample6\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL125	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample6	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400066	GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq	GSM5400066	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL125_6_2.fq.gz Zebrafish_3m_COL125_6_1.fq.gz	fastq fastq	12189015984.0	140103632.0	GSM5400066 r6	0:24 1:150	A:3884770428;C:2485268235;G:2553035720;T:3242414970;N:23526631	24	150	3884770428	2485268235	2553035720	3242414970	23526631	SRX11229458	SRS9283350	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.35675		0.02764		0.87483		0.54135		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64586	64586	SRR14915262	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_1_1.fq.gz Zebrafish_3m_COL124_1_2.fq.gz	fastq fastq	3548358000.0	23655720.0	GSM5400065 r1	0:150 1:150	A:1045459196;C:629224836;G:647117553;T:1223292372;N:3264043	150	150	1045459196	629224836	647117553	1223292372	3264043	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.37097		0.02714		0.83451		0.53691		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64587	64587	SRR14915263	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_2_1.fq.gz Zebrafish_3m_COL124_2_2.fq.gz	fastq fastq	799052400.0	5327016.0	GSM5400065 r2	0:150 1:150	A:224388479;C:154147586;G:159607563;T:260469676;N:439096	150	150	224388479	154147586	159607563	260469676	439096	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.09953		0.00688		0.9361		0.51302		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64588	64588	SRR14915264	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_3_1.fq.gz Zebrafish_3m_COL124_3_2.fq.gz	fastq fastq	1789587900.0	11930586.0	GSM5400065 r3	0:150 1:150	A:504393249;C:331912683;G:346668689;T:603866933;N:2746346	150	150	504393249	331912683	346668689	603866933	2746346	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.16702		0.01095		0.91569		0.53962		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64589	64589	SRR14915265	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_4_1.fq.gz Zebrafish_3m_COL124_4_2.fq.gz	fastq fastq	3069140100.0	20460934.0	GSM5400065 r4	0:150 1:150	A:874150840;C:568413182;G:589948834;T:1033550871;N:3076373	150	150	874150840	568413182	589948834	1033550871	3076373	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.31488		0.01869		0.87444		0.52778		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64590	64590	SRR14915266	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_5_1.fq.gz Zebrafish_3m_COL124_5_2.fq.gz	fastq fastq	15500682600.0	103337884.0	GSM5400065 r5	0:150 1:150	A:4271460153;C:3150814284;G:3316251816;T:4741035876;N:21120471	150	150	4271460153	3150814284	3316251816	4741035876	21120471	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.42634		0.02596		0.86789		0.53869		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64591	64591	SRR14915267	SRX11229457	SRS9283352	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL124	GSM5400065	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL124	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400065	GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq	GSM5400065	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL124_6_1.fq.gz Zebrafish_3m_COL124_6_2.fq.gz	fastq fastq	11909725626.0	136893398.0	GSM5400065 r6	0:24 1:150	A:3806418177;C:2424097718;G:2498410053;T:3158643077;N:22156601	24	150	3806418177	2424097718	2498410053	3158643077	22156601	SRX11229457	SRS9283352	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.39256		0.0232		0.85965		0.51961		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64592	64592	SRR14915256	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_1_1.fq.gz Zebrafish_3m_COL123_1_2.fq.gz	fastq fastq	3807078600.0	25380524.0	GSM5400064 r1	0:150 1:150	A:1122709493;C:680521766;G:695286045;T:1305023708;N:3537588	150	150	1122709493	680521766	695286045	1305023708	3537588	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.35742		0.02244		0.84433		0.53118		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64593	64593	SRR14915257	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_2_1.fq.gz Zebrafish_3m_COL123_2_2.fq.gz	fastq fastq	1538722800.0	10258152.0	GSM5400064 r2	0:150 1:150	A:429732126;C:296572020;G:302968410;T:508614732;N:835512	150	150	429732126	296572020	302968410	508614732	835512	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.13077		0.00804		0.92715		0.53507		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64594	64594	SRR14915258	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_3_1.fq.gz Zebrafish_3m_COL123_3_2.fq.gz	fastq fastq	2031065700.0	13540438.0	GSM5400064 r3	0:150 1:150	A:572071714;C:383932011;G:395219423;T:677149729;N:2692823	150	150	572071714	383932011	395219423	677149729	2692823	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.14905		0.00852		0.92598		0.53922		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64595	64595	SRR14915259	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_4_1.fq.gz Zebrafish_3m_COL123_4_2.fq.gz	fastq fastq	2227611000.0	14850740.0	GSM5400064 r4	0:150 1:150	A:634166526;C:418440499;G:429568047;T:743187782;N:2248146	150	150	634166526	418440499	429568047	743187782	2248146	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.30527		0.01591		0.8873		0.52617		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64596	64596	SRR14915260	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_5_1.fq.gz Zebrafish_3m_COL123_5_2.fq.gz	fastq fastq	17777963700.0	118519758.0	GSM5400064 r5	0:150 1:150	A:4902414982;C:3638996050;G:3803098479;T:5408950692;N:24503497	150	150	4902414982	3638996050	3803098479	5408950692	24503497	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.42515		0.0222		0.87592		0.53827		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64597	64597	SRR14915261	SRX11229456	SRS9283349	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL123	GSM5400064	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL123	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400064	GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq	GSM5400064	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL123_6_1.fq.gz Zebrafish_3m_COL123_6_2.fq.gz	fastq fastq	13923650172.0	160041956.0	GSM5400064 r6	0:24 1:150	A:4482285138;C:2834136946;G:2900635816;T:3680471572;N:26120700	24	150	4482285138	2834136946	2900635816	3680471572	26120700	SRX11229456	SRS9283349	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.38266		0.0197		0.87058		0.53906		24		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64598	64598	SRR14915250	SRX11229455	SRS9283347	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL122	GSM5400063	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL122	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400063	GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq	GSM5400063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL122_1_1.fq.gz Zebrafish_3m_COL122_1_2.fq.gz	fastq fastq	3414690300.0	22764602.0	GSM5400063 r1	0:150 1:150	A:1009187609;C:606970670;G:622677920;T:1172654856;N:3199245	150	150	1009187609	606970670	622677920	1172654856	3199245	SRX11229455	SRS9283347	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.35805		0.02502		0.83887		0.54238		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64599	64599	SRR14915251	SRX11229455	SRS9283347	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL122	GSM5400063	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL122	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400063	GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq	GSM5400063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL122_2_1.fq.gz Zebrafish_3m_COL122_2_2.fq.gz	fastq fastq	888162300.0	5921082.0	GSM5400063 r2	0:150 1:150	A:249596683;C:168975194;G:173081430;T:296037426;N:471567	150	150	249596683	168975194	173081430	296037426	471567	SRX11229455	SRS9283347	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.12808		0.008		0.92178		0.53589		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64600	64600	SRR14915252	SRX11229455	SRS9283347	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL122	GSM5400063	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL122	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400063	GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq	GSM5400063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL122_3_1.fq.gz Zebrafish_3m_COL122_3_2.fq.gz	fastq fastq	1491263400.0	9941756.0	GSM5400063 r3	0:150 1:150	A:420845126;C:278401442;G:289440201;T:500463853;N:2112778	150	150	420845126	278401442	289440201	500463853	2112778	SRX11229455	SRS9283347	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.15632		0.00956		0.91786		0.53197		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64601	64601	SRR14915253	SRX11229455	SRS9283347	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL122	GSM5400063	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL122	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400063	GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq	GSM5400063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL122_4_1.fq.gz Zebrafish_3m_COL122_4_2.fq.gz	fastq fastq	2082366900.0	13882446.0	GSM5400063 r4	0:150 1:150	A:594472285;C:387392031;G:401621477;T:696791581;N:2089526	150	150	594472285	387392031	401621477	696791581	2089526	SRX11229455	SRS9283347	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.30145		0.01747		0.88207		0.53561		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures
64602	64602	SRR14915254	SRX11229455	SRS9283347	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 3m COL122	GSM5400063	source name:Zebrafish 3m sample5\|strain:AB\|age:3 month 90 day\|tissue:whole organism	Microwell seq datasets of Zebrafish 3m COL122	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 3m sample5	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:3 month 90 day\|tissue:whole organism	GSM5400063	GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq	GSM5400063	1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000		Zebrafish_3m_COL122_5_1.fq.gz Zebrafish_3m_COL122_5_2.fq.gz	fastq fastq	14497371300.0	96649142.0	GSM5400063 r5	0:150 1:150	A:3998637379;C:2959163742;G:3108117704;T:4411762861;N:19689614	150	150	3998637379	2959163742	3108117704	4411762861	19689614	SRX11229455	SRS9283347	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	1	0.42459		0.02409		0.87008		0.53134		150		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-06-25	Adult	Adult	Whole Organism	All anatomical structures

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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");;