run_metadata: 66222

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
66222	SRR16148348	SRX12433220	SRS10400589	SRP339629	PRJNA767802	RNA seq and ATAC seq of WT and Gli3 / zebrafish	PRJNA767802	Other	WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.			Replicate 3 RNAseq Gli3 /		RNAseq Gli3KO 3		strain:Gli3 / ex5 3\|dev stage:55hpf\|sex:NA\|tissue:EGFP cells\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio: Gli3 / EGFP cells	6	6	Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.			RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP339629		assembly:GRCz11	Gli3KO3_aligned.sorted.bam	bam	5067915101.0	25431299.0	Gli3KO3 aligned.sorted.bam	0:99.63 1:99.65	A:1368455893;C:1172445678;G:1173478123;T:1353535407;N:0	99	99			1368455893	1172445678	1173478123	1353535407	0	SRX12433220	SRS10400589	SRA1303956	Rutgers University\|Genetics	Rutgers University	2	0.95469	0.95749	0.09504	0.09606	0.73951	0.73963	0.54439	0.54442	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown		United States	2021-10-01	Hatching	Embryo	Undetermined	Embryo Imprecise