metadata: run_metadata: 6 rows where devstage_curation = "Undetermined" and technology = "marsseq"

6 rows where devstage_curation = "Undetermined" and technology = "marsseq"

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.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
53255	53255	SRR9825000	SRX6581675	SRS5147373	SRP216247	PRJNA556201	Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq	GSE134706	Other	Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. The raw data for human subjects will be submitted through EGA for controlled access.	parent bioproject:PRJNA556197	pubmed:31835035	MP 15 fish 3A.M	GSM3963911	source name:Total brain\|strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|age:4 5mo	MP 15 fish 3A.M	Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: text files include mRNA molecule count values for each Sample	Total brain	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|catalog #:I32450\|age:4 5mo	GSM3963911	GSM3963911: MP 15 fish 3A.M; Danio rerio; RNA Seq	GSM3963911		1	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP216247	loader:fastq load.py\|options: appendBCtoName	MP_15_fish_3A.M.fastq.gz	fastq	438550950.0	5847346.0	GSM3963911 r1	0:75	A:133219954;C:87024588;G:96110755;T:122193517;N:2136	75		133219954	87024588	96110755	122193517	2136	SRX6581675	SRS5147373	SRA926015	GEO	Immunology, Weizmann Institute of Science	1	0.85665		0.14851		0.83855		0.48702	75		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	marsseq	Israel	2019-07-23	Undetermined	Undetermined	Brain	Nervous System
53256	53256	SRR9824999	SRX6581674	SRS5147372	SRP216247	PRJNA556201	Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq	GSE134706	Other	Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. The raw data for human subjects will be submitted through EGA for controlled access.	parent bioproject:PRJNA556197	pubmed:31835035	MP 14 fish 2A.M	GSM3963910	source name:Total brain\|strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|age:4 5mo	MP 14 fish 2A.M	Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: text files include mRNA molecule count values for each Sample	Total brain	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|catalog #:I32450\|age:4 5mo	GSM3963910	GSM3963910: MP 14 fish 2A.M; Danio rerio; RNA Seq	GSM3963910		1	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP216247	loader:fastq load.py\|options: appendBCtoName	MP_14_fish_2A.M.fastq.gz	fastq	581871000.0	7758280.0	GSM3963910 r1	0:75	A:177443331;C:113767797;G:126832616;T:163824391;N:2865	75		177443331	113767797	126832616	163824391	2865	SRX6581674	SRS5147372	SRA926015	GEO	Immunology, Weizmann Institute of Science	1	0.8556		0.15773		0.8356		0.47849	75		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	marsseq	Israel	2019-07-23	Undetermined	Undetermined	Brain	Nervous System
53257	53257	SRR9824998	SRX6581673	SRS5147371	SRP216247	PRJNA556201	Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq	GSE134706	Other	Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. The raw data for human subjects will be submitted through EGA for controlled access.	parent bioproject:PRJNA556197	pubmed:31835035	MP 13 fish 1A.M	GSM3963909	source name:Total brain\|strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|age:4 5mo	MP 13 fish 1A.M	Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: text files include mRNA molecule count values for each Sample	Total brain	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	strain:WT\|tissue:Brain\|selection markers:Ib4+\|source:Thermo Fisher\|catalog #:I32450\|age:4 5mo	GSM3963909	GSM3963909: MP 13 fish 1A.M; Danio rerio; RNA Seq	GSM3963909		1	10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP216247	loader:fastq load.py\|options: appendBCtoName	MP_13_fish_1A.M.fastq.gz	fastq	744772275.0	9930297.0	GSM3963909 r1	0:75	A:222652841;C:152631684;G:170650353;T:198833897;N:3500	75		222652841	152631684	170650353	198833897	3500	SRX6581673	SRS5147371	SRA926015	GEO	Immunology, Weizmann Institute of Science	1	0.87523		0.10463		0.84812		0.5271	75		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	marsseq	Israel	2019-07-23	Undetermined	Undetermined	Brain	Nervous System
68656	68656	SRR18097957	SRX14248907	SRS12068875	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells		pubmed:35614218	Immature fin ECs plate3	GSM5910460	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate3	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910460	GSM5910460: Immature fin ECs plate3; Danio rerio; RNA Seq	GSM5910460 r1	GSM5910460	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC3_S0_R1_001.fastq.gz BC3_S0_R2_001.fastq.gz	fastq fastq	5000226570.0	55558073.0	GSM5910460 r1	0:75 1:15	A:1398279779;C:1105834990;G:1278168650;T:1217071842;N:871309	75	15	1398279779	1105834990	1278168650	1217071842	871309	SRX14248907	SRS12068875	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.75587	0.0	0.22384	0.0	0.87665	1.0	0.59533	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure
68657	68657	SRR18097958	SRX14248906	SRS12068874	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells		pubmed:35614218	Immature fin ECs plate2	GSM5910459	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate2	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910459	GSM5910459: Immature fin ECs plate2; Danio rerio; RNA Seq	GSM5910459 r1	GSM5910459	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC2_S0_R1_001.fastq.gz BC2_S0_R2_001.fastq.gz	fastq fastq	4158365400.0	46204060.0	GSM5910459 r1	0:75 1:15	A:1056133752;C:954371027;G:1117373354;T:1029764959;N:722308	75	15	1056133752	954371027	1117373354	1029764959	722308	SRX14248906	SRS12068874	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.76282	0.0	0.2382	0.0	0.87158	1.0	0.53888	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure
68658	68658	SRR18097959	SRX14248905	SRS12068873	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells		pubmed:35614218	Immature fin ECs plate1	GSM5910458	source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate1	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910458	GSM5910458: Immature fin ECs plate1; Danio rerio; RNA Seq	GSM5910458 r1	GSM5910458	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP360907		BC1_S0_R1_001.fastq.gz BC1_S0_R2_001.fastq.gz	fastq fastq	4284501750.0	47605575.0	GSM5910458 r1	0:75 1:15	A:1172578653;C:976724863;G:1071723716;T:1062724053;N:750465	75	15	1172578653	976724863	1071723716	1062724053	750465	SRX14248905	SRS12068873	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.73652	0.0	0.20176	0.0	0.86622	1.0	0.66697	75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure

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