metadata: run_metadata: 9 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "indrops"

9 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "indrops"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
74455	74455	SRR23804140	SRX19635460	SRS17004492	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	kdrl:GFP+ adult kidney	GSM7091842	source name:kdrl:GFP transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:GFP+ adult kidney	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091842	GSM7091842: kdrl:GFP+ adult kidney; Danio rerio; RNA Seq	GSM7091842 r1	GSM7091842	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651	FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz	fastq	10648313404.0	80407702.0	GSM7091842 r1	0:132.43	A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564	132	3393628100	2087372845	1953079760	3213786135	446564	SRX19635460	SRS17004492	Oncology/Hematology, Boston Children's Hospital	1	0.60891	0.10525	0.81903	0.52577	150	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
74456	74456	SRR23804141	SRX19635459	SRS17004491	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	kdrl:mCherry+ adult kidney rep2	GSM7091841	source name:kdrl:mCherry transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:mCherry+ adult kidney rep2	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:mCherry transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091841	GSM7091841: kdrl:mCherry+ adult kidney rep2; Danio rerio; RNA Seq	GSM7091841 r1	GSM7091841	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651	FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz	fastq	13922952441.0	105098464.0	GSM7091841 r1	0:132.48	A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654	132	4341235438	2807868369	2579519980	4193742000	586654	SRX19635459	SRS17004491	Oncology/Hematology, Boston Children's Hospital	1	0.64512	0.12315	0.81712	0.52922	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
74457	74457	SRR23804142	SRX19635458	SRS17004490	SRP426651	PRJNA943248	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]	GSE227115	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	kdrl:mCherry+ adult kidney rep1	GSM7091840	source name:kdrl:mCherry transgenic zebrafish adult kidney wild type\|developmental stage:adult\|genotype:wild type\|tissue:kidney	kdrl:mCherry+ adult kidney rep1	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:mCherry transgenic zebrafish adult kidney wild type	No treatments	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	developmental stage:adult\|genotype:wild type\|tissue:kidney	GSM7091840	GSM7091840: kdrl:mCherry+ adult kidney rep1; Danio rerio; RNA Seq	GSM7091840 r1	GSM7091840	1	Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426651	KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz	fastq	8774502682.0	64692571.0	GSM7091840 r1	0:135.63	A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111	135	2791773089	1725088037	1633088372	2624197073	356111	SRX19635458	SRS17004490	Oncology/Hematology, Boston Children's Hospital	1	0.66981	0.10372	0.81357	0.5394	38	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Adult	Adult	Kidney	Renal System
74458	74458	SRR23802705	SRX19634573	SRS17003744	SRP426627	PRJNA943249	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]	GSE227117	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized filtered and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2	GSM7091919	source name:kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type\|tissue:embryos\|genotype:wild type	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type	No treatments	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	tissue:embryos\|genotype:wild type	GSM7091919	GSM7091919: kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2; Danio rerio; RNA Seq	GSM7091919 r1	GSM7091919	1	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426627	GR4_Single_Cell_TCTTACGC.fastq.sorted.fastq.gz	fastq	13661225700.0	102550405.0	GSM7091919 r1	0:133.21	A:4263167363;C:2771561232;G:2605236063;T:4020689114;N:571928	133	4263167363	2771561232	2605236063	4020689114	571928	SRX19634573	SRS17003744	Oncology/Hematology, Boston Children's Hospital	1	0.64929	0.08349	0.80462	0.50638	149	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Embryo Imprecise	All anatomical structures
74459	74459	SRR23802706	SRX19634572	SRS17003743	SRP426627	PRJNA943249	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]	GSE227117	Transcriptome Analysis	We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized filtered and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1	GSM7091918	source name:kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type\|tissue:embryos\|genotype:wild type	kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type	No treatments	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells.	tissue:embryos\|genotype:wild type	GSM7091918	GSM7091918: kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1; Danio rerio; RNA Seq	GSM7091918 r1	GSM7091918	1	Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426627	GR_Single_Cell_AGGCTTAG.fastq.sorted.fastq.gz	fastq	15177402828.0	110023820.0	GSM7091918 r1	0:137.95	A:4661865038;C:2940634835;G:2919070311;T:4655218796;N:613848	137	4661865038	2940634835	2919070311	4655218796	613848	SRX19634572	SRS17003743	Oncology/Hematology, Boston Children's Hospital	1	0.73316	0.12888	0.79594	0.5247	127	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Embryo Imprecise	All anatomical structures
74460	74460	SRR23802569	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L001.fastq.sorted.fastq.gz	fastq	715456535.0	12017381.0	GSM7091920 r1	0:59.54	A:205982879;C:141307848;G:135221384;T:232940601;N:3823	59	205982879	141307848	135221384	232940601	3823	SRX19634451	SRS17003621	Oncology/Hematology, Boston Children's Hospital	1	0.88315	0.14516	0.78257	0.49661	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74461	74461	SRR23802570	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz	fastq	589786185.0	9927008.0	GSM7091920 r2	0:59.41	A:170171480;C:115960508;G:111370241;T:192283114;N:842	59	170171480	115960508	111370241	192283114	842	SRX19634451	SRS17003621	Oncology/Hematology, Boston Children's Hospital	1	0.88418	0.1452	0.78173	0.48617	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74462	74462	SRR23802571	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L003.fastq.sorted.fastq.gz	fastq	683131915.0	11477240.0	GSM7091920 r3	0:59.52	A:196805573;C:134822600;G:129142852;T:222358115;N:2775	59	196805573	134822600	129142852	222358115	2775	SRX19634451	SRS17003621	Oncology/Hematology, Boston Children's Hospital	1	0.88169	0.14457	0.78054	0.49459	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system
74463	74463	SRR23802572	SRX19634451	SRS17003621	SRP426621	PRJNA943252	Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]	GSE227118	Other	We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.	parent bioproject:PRJNA510836	Whole tail 72 hpf	GSM7091920	source name:transgenic zebrafish embryos wild type\|tissue:Whole tail\|developmental stage:72 hpf	Whole tail 72 hpf	the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode	transgenic zebrafish embryos wild type	No treatments	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells.	tissue:Whole tail\|developmental stage:72 hpf	GSM7091920	GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq	GSM7091920 r1	GSM7091920	1	Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426621	EH_Tails_Single_Cell_GAGACGGA_L004.fastq.sorted.fastq.gz	fastq	584432554.0	9840065.0	GSM7091920 r4	0:59.39	A:168684456;C:114891950;G:110562368;T:190292465;N:1315	59	168684456	114891950	110562368	190292465	1315	SRX19634451	SRS17003621	Oncology/Hematology, Boston Children's Hospital	1	0.88266	0.14397	0.78001	0.49223	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Tail	Multi-system

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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");;