metadata: run_metadata: 6 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "generic-scrnaseq-only"

6 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "generic-scrnaseq-only"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	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.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
26536	26536	SRR26130973	SRX21844394	SRS18942411	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X49 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 6\|BioSampleModel:Model organism or animal	SC ZF Hypo6	10X49 2	10X49 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X49_2_S5_L001_R1_001.fastq.gz 10X49_2_S5_L001_R2_001.fastq.gz 10X49_2_S5_L002_R1_001.fastq.gz 10X49_2_S5_L002_R2_001.fastq.gz 10X49_2_S5_L003_R1_001.fastq.gz 10X49_2_S5_L003_R2_001.fastq.gz 10X49_2_S5_L004_R1_001.fastq.gz 10X49_2_S5_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3126113844.0	37215641.0	10X49 2 S5 L001 R1 001.fastq.gz	0:28 1:56	A:898881980;C:657306128;G:664563758;T:905262774;N:99204	28	56	898881980	657306128	664563758	905262774	99204	SRX21844394	SRS18942411	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01241	0.88203	0.00542	0.35268	0.98129	0.7586	0.40274	0.5074	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26537	26537	SRR26130974	SRX21844393	SRS18942407	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X49 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 5\|BioSampleModel:Model organism or animal	SC ZF Hypo5	10X49 1	10X49 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X49_1_S4_L001_R1_001.fastq.gz 10X49_1_S4_L001_R2_001.fastq.gz 10X49_1_S4_L002_R1_001.fastq.gz 10X49_1_S4_L002_R2_001.fastq.gz 10X49_1_S4_L003_R1_001.fastq.gz 10X49_1_S4_L003_R2_001.fastq.gz 10X49_1_S4_L004_R1_001.fastq.gz 10X49_1_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3315364752.0	39468628.0	10X49 1 S4 L001 R1 001.fastq.gz	0:28 1:56	A:957164498;C:690985782;G:704099796;T:963009918;N:104758	28	56	957164498	690985782	704099796	963009918	104758	SRX21844393	SRS18942407	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.0143	0.88325	0.00601	0.35854	0.97816	0.75868	0.4158	0.50825	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26538	26538	SRR26130975	SRX21844392	SRS18942399	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X47 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 4\|BioSampleModel:Model organism or animal	SC ZF Hypo4	10X47 2	10X47 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X47_2_S2_L001_R1_001.fastq.gz 10X47_2_S2_L001_R2_001.fastq.gz 10X47_2_S2_L002_R1_001.fastq.gz 10X47_2_S2_L002_R2_001.fastq.gz 10X47_2_S2_L003_R1_001.fastq.gz 10X47_2_S2_L003_R2_001.fastq.gz 10X47_2_S2_L004_R1_001.fastq.gz 10X47_2_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3525979800.0	41975950.0	10X47 2 S2 L001 R1 001.fastq.gz	0:28 1:56	A:1030048762;C:725438274;G:855378888;T:915005070;N:108806	28	56	1030048762	725438274	855378888	915005070	108806	SRX21844392	SRS18942399	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.0126	0.69252	0.00546	0.25721	0.98005	0.85295	0.39068	0.51992	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26539	26539	SRR26130976	SRX21844391	SRS18942406	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X47 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 3\|BioSampleModel:Model organism or animal	SC ZF Hypo3	10X47 1	10X47 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X47_1_S1_L001_R1_001.fastq.gz 10X47_1_S1_L001_R2_001.fastq.gz 10X47_1_S1_L002_R1_001.fastq.gz 10X47_1_S1_L002_R2_001.fastq.gz 10X47_1_S1_L003_R1_001.fastq.gz 10X47_1_S1_L003_R2_001.fastq.gz 10X47_1_S1_L004_R1_001.fastq.gz 10X47_1_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	3288490212.0	39148693.0	10X47 1 S1 L001 R1 001.fastq.gz	0:28 1:56	A:950740376;C:692224998;G:723085676;T:922337432;N:101730	28	56	950740376	692224998	723085676	922337432	101730	SRX21844391	SRS18942406	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01086	0.86383	0.0052	0.31674	0.98244	0.78309	0.39399	0.52299	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26540	26540	SRR26130977	SRX21844390	SRS18942410	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X39 2	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 2\|BioSampleModel:Model organism or animal	SC ZF Hypo2	10X39 2	10X39 2	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X39_2_S2_L001_R1_001.fastq.gz 10X39_2_S2_L001_R2_001.fastq.gz 10X39_2_S2_L002_R1_001.fastq.gz 10X39_2_S2_L002_R2_001.fastq.gz 10X39_2_S2_L003_R1_001.fastq.gz 10X39_2_S2_L003_R2_001.fastq.gz 10X39_2_S2_L004_R1_001.fastq.gz 10X39_2_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	20594785932.0	245176023.0	10X39 2 S2 L001 R1 001.fastq.gz	0:28 1:56	A:5909286071;C:4378110318;G:4489721587;T:5804002561;N:13665395	28	56	5909286071	4378110318	4489721587	5804002561	13665395	SRX21844390	SRS18942410	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01117	0.90005	0.00416	0.25843	0.98056	0.77926	0.45338	0.53366	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	Brain	Nervous System
26541	26541	SRR26130978	SRX21844389	SRS18942405	SRP462307	PRJNA1019490	Single Cell RNA seq of Zebrafish Hypothalamus	PRJNA1019490	Other	Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates.	10X39 1	breed:NA\|age:Adult\|collection date:2021\|geo loc name:Israel\|sex:not applicable\|tissue:Brain Hypothalamus\|sample type:single cell 1\|BioSampleModel:Model organism or animal	SC ZF Hypo1	10X39 1	10X39 1	we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP462307	10X39_1_S1_L004_R2_001.fastq.gz 10X39_1_S1_L004_R1_001.fastq.gz 10X39_1_S1_L003_R2_001.fastq.gz 10X39_1_S1_L003_R1_001.fastq.gz 10X39_1_S1_L002_R2_001.fastq.gz 10X39_1_S1_L002_R1_001.fastq.gz 10X39_1_S1_L001_R2_001.fastq.gz 10X39_1_S1_L001_R1_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	13293718116.0	158258549.0	10X39 1 S1 L001 R1 001.fastq.gz	0:28 1:56	A:3791388201;C:2833705086;G:2863082386;T:3796683434;N:8859009	28	56	3791388201	2833705086	2863082386	3796683434	8859009	SRX21844389	SRS18942405	SRA1717104	Technion - Israel Institute of Technology\|Neuroscince	Technion - Israel Institute of Technology	2	0.01078	0.90504	0.00392	0.24179	0.98098	0.77741	0.42922	0.52858	28	56	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_generic	generic-scrnaseq-only	Israel	2023-09-21	Adult	Adult	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");;