metadata: run_metadata: 3 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "marsseq" and tissue

3 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "marsseq" and tissue_curation = "Brain"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.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.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.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
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

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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");;