run_metadata: 60453

This data as json

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
60453	SRR12283716	SRX8787095	SRS7055742	SRP273008	PRJNA647599	Transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo	GSE154885	Transcriptome Analysis	cDNA extracted from FACS sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBACnkx2.2a:memGFP TgBAColig2:GFP or TgBACdbx1b:GFP Overall design: transcriptome of nkx2.2a+ olig2+ dbx1b+ cells from 14hpf zebrafish embryo		pubmed:33004519		TgBAColig2:GFP positive cells 2	GSM4681844		tissue:FACS sorted olig2 + neural progenitors\|age:14hpf\|genotype:WT	TgBAColig2:GFP positive cells 2	Sequenced reads were filtered by fastqc 0.11.3 then mapped to GRCz10 whole genome using bowtie 1.1.1 with parameters q n 2 l 28 e 1000 I 0 X 1000 k 1 m 200 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include gene names gene length mapped count unmapped count Supplementary files format and content: excel spreadsheet with gene names and transcript count in each sample	FACS sorted olig2 + neural progenitors		14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols		age:14hpf\|genotype:WT	GSM4681844	GSM4681844: TgBAColig2:GFP positive cells 2; Danio rerio; RNA Seq	GSM4681844		1	14hpf zebrafish embryos were dissected to remove the brain and tail region. The trunk region is dissociated by mechanical pipetting in FACSMax solution. The dissociated cells are resuspended in PBS FACS sorted for GFP positive cells. The sorted cells are spun down and the pellet was flash frozen in Trizol for RNA extraction. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4681844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP273008			LIB018768_TRA00046535_S12_L002_R1.fastq LIB018768_TRA00046535_S12_L002_R2.fastq	fastq fastq	1883562500.0	18835625.0	GSM4681844 r1	0:50 1:50	A:538880974;C:389273777;G:399233943;T:555933855;N:239951	50	50			538880974	389273777	399233943	555933855	239951	SRX8787095	SRS7055742	SRA1102160	GEO	Sean Megason, Systems Biology, Harvard Medical School	2	0.83434	0.81762	0.28607	0.27612	0.77804	0.78137	0.67234	0.67724	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		United States	2020-07-22	Segmentation	Embryo	Multi-tissue	Multi-system