metadata: run_metadata: 1 row where technology = "celseq" and tissue

1 row where technology = "celseq" and tissue_curation = "Tail"

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.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	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.r3_length	run.r4_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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
50874	50874	SRR8356798	SRX5167561	SRS4175446	SRP173971	PRJNA510841	Transcription factor induction of vascular blood stem cell niches in vivo [TOMO Seq]	GSE124150	Other	We report RNA tomography tomo seq gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue CHT was isolated by manual dissection snap froze and then cryosections 40 in total 8 µm thick were collected along the dorsal ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing. Overall design: The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method Junker et al. 2014.	parent bioproject:PRJNA510836			Tomo seq zebrafish tail at 72 hpf	GSM3521717		source name:mpx:GFP transgenic zebrafish embryo wild type Casper background\|tissue:tail\|developmental stage:72 hpf	Tomo seq zebrafish tail at 72 hpf	Library strategy: RNA tomography tomo seq Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the Junker et al. 2014. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Mapping and demultiplexing were done as described in Grün et al. Validation of noise models for single cell transcriptomics Nature Methods 2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0 where script tomo.sh is an example for how to run the mapping scripts. Genome build: zv9	mpx:GFP transgenic zebrafish embryo wild type Casper background	No treatment	The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.	mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice.	tissue:tail\|developmental stage:72 hpf	GSM3521717	GSM3521717: Tomo seq zebrafish tail at 72 hpf; Danio rerio; OTHER	GSM3521717		1	The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.	GEO Accession:GSM3521717	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP173971					3762222874.0	24959737.0	GSM3521717 r1	0:75.36 1:75.37	A:1160852277;C:485683733;G:556965887;T:1558649449;N:71528	75	75			1160852277	485683733	556965887	1558649449	71528	SRX5167561	SRS4175446	SRA825234	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.20644	0.76788	0.14917	0.11551	0.98169	0.8382	0.50072	0.52728	76	76	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	other	unknown	sc	single_cell_plate	celseq		United States	2018-12-19	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");;