run_metadata: 8100

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
8100	ERR2402424	ERX2443278	ERS2295352	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693969	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693969\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM4\|common name:zebrafish\|sample name:CM4\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500		ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz	fastq fastq	5803404091.0	41335851.0	ena RUN DPSQ 14 03 2018 19:09:09:420 4	0:70.72 1:69.67	A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888	70	69			1590577583	1305683925	1331895549	1575219146	27888	ERX2443278	ERS2295352	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.9216	0.91971	0.05719	0.05738	0.77333	0.77761	0.47789	0.47244	76	74	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown		United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System