metadata: run_metadata: 8 rows where devstage_curation_coarse = "Multi-stage" and tissue

8 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Skin"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.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
25298	25298	SRR25764100	SRX21486771	SRS18719071	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf itgb4+ embryonic basal precursors rep2	GSM7734878	tissue:epidermal cells\|cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry\|geo loc name:missing\|collection date:missing	1 dpf itgb4+ embryonic basal precursors rep2	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry	GSM7734878	GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq	GSM7734878 r1	GSM7734878	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz	fastq fastq	6040245600.0	15100614.0	GSM7734878 r1	0:200 1:200	A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625	200	200	1588346322	1356558310	1524614760	1569583583	1142625	SRX21486771	SRS18719071	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.0156	0.0191	0.00074	0.00093	0.99024	0.99088	0.47058	0.47838	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25299	25299	SRR25764101	SRX21486770	SRS18719070	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf itgb4+ embryonic basal precursors rep1	GSM7734877	tissue:epidermal cells\|cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry\|geo loc name:missing\|collection date:missing	1 dpf itgb4+ embryonic basal precursors rep1	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry	GSM7734877	GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq	GSM7734877 r1	GSM7734877	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz	fastq fastq	7055215600.0	17638039.0	GSM7734877 r1	0:200 1:200	A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146	200	200	1894635584	1556854856	1769420212	1825520802	8784146	SRX21486770	SRS18719070	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01135	0.01881	0.00043	0.00016	0.9932	0.99543	0.46234	0.43106	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25300	25300	SRR25764102	SRX21486769	SRS18719069	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf krt4+ embryonic periderm cells rep2	GSM7734876	tissue:epidermal cells\|cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp\|geo loc name:missing\|collection date:missing	1 dpf krt4+ embryonic periderm cells rep2	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp	GSM7734876	GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq	GSM7734876 r1	GSM7734876	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz	fastq fastq	9439207600.0	23598019.0	GSM7734876 r1	0:200 1:200	A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207	200	200	2499982675	2086665360	2395002073	2454282285	3275207	SRX21486769	SRS18719069	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.44931	0.01877	0.02236	0.00115	0.80012	0.99032	0.45473	0.49453	200	200	B	T	mate2 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25301	25301	SRR25764103	SRX21486768	SRS18719066	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf krt4+ embryonic periderm cells rep1	GSM7734875	tissue:epidermal cells\|cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp\|geo loc name:missing\|collection date:missing	1 dpf krt4+ embryonic periderm cells rep1	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp	GSM7734875	GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq	GSM7734875 r1	GSM7734875	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz	fastq fastq	6119547200.0	15298868.0	GSM7734875 r1	0:200 1:200	A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992	200	200	1642059769	1349462427	1535937964	1584527048	7559992	SRX21486768	SRS18719066	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01112	0.01017	0.0003	0.00014	0.9931	0.99586	0.43605	0.40821	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
52154	52154	SRR18181452	SRX14328416	SRS12144047	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Skin6	GSM5924290	source name:skin\|strain:Tubingen\|tissue:skin\|genotype:wild type	Skin6	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	skin		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:skin\|genotype:wild type	GSM5924290	GSM5924290: Skin6; Danio rerio; RNA Seq	GSM5924290		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924290	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Skin6.bam	bam	25513490100.0	85044967.0	GSM5924290 r1	0:150 1:150	A:6925113942;C:3968740165;G:4171395948;T:10445470654;N:2769391	150	150	6925113942	3968740165	4171395948	10445470654	2769391	SRX14328416	SRS12144047	SRA880843	GEO	Zhejiang University	2	2e-05	0.59157	0.0	0.06443	0.99997	0.87677	1.0	0.63522	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Skin	Surface Structure
52155	52155	SRR18181451	SRX14328415	SRS12144046	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Skin5	GSM5924289	source name:skin\|strain:Tubingen\|tissue:skin\|genotype:wild type	Skin5	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	skin		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:skin\|genotype:wild type	GSM5924289	GSM5924289: Skin5; Danio rerio; RNA Seq	GSM5924289		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924289	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Skin5.bam	bam	28489208700.0	94964029.0	GSM5924289 r1	0:150 1:150	A:8246685822;C:4290659458;G:4422543987;T:11526089448;N:3229985	150	150	8246685822	4290659458	4422543987	11526089448	3229985	SRX14328415	SRS12144046	SRA880843	GEO	Zhejiang University	2	0.0	0.52	0.0	0.05199	1.0	0.89509		0.61209	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Skin	Surface Structure
52156	52156	SRR18181450	SRX14328414	SRS12144045	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Skin3	GSM5924288	source name:skin\|strain:Tubingen\|tissue:skin\|genotype:wild type	Skin3	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	skin		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:skin\|genotype:wild type	GSM5924288	GSM5924288: Skin3; Danio rerio; RNA Seq	GSM5924288		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924288	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Skin3.bam	bam	22656818700.0	75522729.0	GSM5924288 r1	0:150 1:150	A:5656101080;C:3775541088;G:3901788913;T:9321421770;N:1965849	150	150	5656101080	3775541088	3901788913	9321421770	1965849	SRX14328414	SRS12144045	SRA880843	GEO	Zhejiang University	2	2e-05	0.77804	0.0	0.0376	0.99997	0.77275	1.0	0.58426	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Skin	Surface Structure
52201	52201	SRR8991405	SRX5770473	SRS4704582	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Skin4	GSM3740958	source name:skin\|strain:Tubingen\|genotype:wild type\|tissue:skin	Skin4	The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	skin		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype:wild type\|tissue:skin	GSM3740958	GSM3740958: Skin4; Danio rerio; RNA Seq	GSM3740958		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3740958	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10	Skin4.bam	bam	33628232728.0	111351764.0	GSM3740958 r1	0:151 1:151	A:8460681247;C:5738320863;G:5953293918;T:13386336300;N:89600400	151	151	8460681247	5738320863	5953293918	13386336300	89600400	SRX5770473	SRS4704582	SRA880843	GEO	Zhejiang University	2	0.0	0.73034	0.0	0.03701	1.0	0.80454		0.53563	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-04-30	Undetermined	Multi-stage	Skin	Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

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");;