metadata: run_metadata: 5 rows where experiment.platform = "DNBSEQ", technology = "10x" and tissue_curation

5 rows where experiment.platform = "DNBSEQ", technology = "10x" 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.library_name	experiment.design_description	experiment.library_construction_protocol	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
64514	64514	SRR17137062	SRX13321492	SRS11229253	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 COL104	GSM5718328	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL104	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	GSM5718328	GSM5718328: Microwell seq datasets of Zebrafish 72hpf COL104; Danio rerio; RNA Seq	GSM5718328		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_COL104.bam	10X Genomics bam file	90497447328.0	520100272.0	GSM5718328 r1	0:24 1:150	A:26568037621;C:19526761960;G:20762820842;T:23593883403;N:45943502	24	150	26568037621	19526761960	20762820842	23593883403	45943502	SRX13321492	SRS11229253	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00219	0.7651	0.00205	0.0914	0.99981	0.79953	0.5	0.51979	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
69032	69032	SRR18915949	SRX14993867	SRS12743200	SRP363983	PRJNA816047	Mapping the zebrafish developmental and aging atlas by single cell mRNA seq	GSE198571	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA817101	pubmed:35929025	Micorwell seq datasets of Zebrafish 21d COL79	GSM6065255	source name:Zebrafish 21d sample1\|strain:AB\|age:21 day\|tissue:whole organism	Micorwell seq datasets of Zebrafish 21d COL79	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 21d sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:21 day\|tissue:whole organism	GSM6065255	GSM6065255: Micorwell seq datasets of Zebrafish 21d COL79; Danio rerio; RNA Seq	GSM6065255 r1	GSM6065255	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	SRP363983	assembly:GRCz11\|intentional duplicate	Zebrafish_21d_COL79.bam	10X Genomics bam file	141397811748.0	812631102.0	GSM6065255 r1	0:24 1:150	A:42419601578;C:30491813752;G:32301586155;T:36094049456;N:90760807	24	150	42419601578	30491813752	32301586155	36094049456	90760807	SRX14993867	SRS12743200	SRA1409755	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00187	0.69179	0.00172	0.07347	0.99975	0.82231	0.33333	0.52514	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-04-25	Larval	Larval	Whole Organism	All anatomical structures
69035	69035	SRR18915952	SRX14993864	SRS12743197	SRP363983	PRJNA816047	Mapping the zebrafish developmental and aging atlas by single cell mRNA seq	GSE198571	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA817101	pubmed:35929025	Micorwell seq datasets of Zebrafish 21d COL76	GSM6065252	source name:Zebrafish 21d sample1\|strain:AB\|age:21 day\|tissue:whole organism	Micorwell seq datasets of Zebrafish 21d COL76	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 21d sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:21 day\|tissue:whole organism	GSM6065252	GSM6065252: Micorwell seq datasets of Zebrafish 21d COL76; Danio rerio; RNA Seq	GSM6065252 r1	GSM6065252	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	SRP363983	assembly:GRCz11\|intentional duplicate	Zebrafish_21d_COL76.bam	10X Genomics bam file	111633243510.0	641570365.0	GSM6065252 r1	0:24 1:150	A:33972927532;C:23914299609;G:25579933876;T:28104989997;N:61092496	24	150	33972927532	23914299609	25579933876	28104989997	61092496	SRX14993864	SRS12743197	SRA1409755	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00193	0.6842	0.00182	0.07841	0.99983	0.82059	0.375	0.55944	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-04-25	Larval	Larval	Whole Organism	All anatomical structures
69038	69038	SRR18642995	SRX14746259	SRS12507764	SRP363983	PRJNA816047	Mapping the zebrafish developmental and aging atlas by single cell mRNA seq	GSE198571	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA817101	pubmed:35929025	Micorwell seq datasets of Zebrafish 21d COL73	GSM6019658	source name:Zebrafish 21d sample1\|strain:AB\|age:21 day\|tissue:whole organism	Micorwell seq datasets of Zebrafish 21d COL73	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 21d sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:21 day\|tissue:whole organism	GSM6019658	GSM6019658: Micorwell seq datasets of Zebrafish 21d COL73; Danio rerio; RNA Seq	GSM6019658 r1	GSM6019658	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	SRP363983	assembly:GRCz11\|intentional duplicate	Zebrafish_21d_COL73.bam	10X Genomics bam file	94495251666.0	543076159.0	GSM6019658 r1	0:24 1:150	A:28813859102;C:20196407259;G:21422570931;T:24009240216;N:53174158	24	150	28813859102	20196407259	21422570931	24009240216	53174158	SRX14746259	SRS12507764	SRA1398049	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.002	0.68935	0.00186	0.07467	0.99977	0.82392	0.45454	0.54871	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-04-05	Larval	Larval	Whole Organism	All anatomical structures
69040	69040	SRR18642997	SRX14746257	SRS12507765	SRP363983	PRJNA816047	Mapping the zebrafish developmental and aging atlas by single cell mRNA seq	GSE198571	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA817101	pubmed:35929025	Micorwell seq datasets of Zebrafish 21d COL71	GSM6019656	source name:Zebrafish 21d sample1\|strain:AB\|age:21 day\|tissue:whole organism	Micorwell seq datasets of Zebrafish 21d COL71	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 21d sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	strain:AB\|age:21 day\|tissue:whole organism	GSM6019656	GSM6019656: Micorwell seq datasets of Zebrafish 21d COL71; Danio rerio; RNA Seq	GSM6019656 r1	GSM6019656	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	SRP363983	assembly:GRCz11\|intentional duplicate	Zebrafish_21d_COL71.bam	10X Genomics bam file	141830365482.0	815117043.0	GSM6019656 r1	0:24 1:150	A:43213881758;C:30298104199;G:32190676130;T:36046592777;N:81110618	24	150	43213881758	30298104199	32190676130	36046592777	81110618	SRX14746257	SRS12507765	SRA1398049	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00172	0.68841	0.00159	0.06954	0.99977	0.82351	0.54545	0.55717	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-04-05	Larval	Larval	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");;