run_metadata: 36384

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
36384	SRR514028	SRX155008	SRS346294	SRP013815	PRJNA168635	Id2a knockdown in zebrafish retina	GSE38786	Transcriptome Analysis	During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples		pubmed:22981606		Zebrafish retina with Id2aMM morpholino treatment replicate 1	GSM949494		source name:Zebrafish retina with Id2aMM morpholino treatment replicate 1\|tissue:retina\|genotype/variation:control	Zebrafish retina with Id2aMM morpholino treatment replicate 1	Filter out all reads with no call ‘N’ and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes.	Zebrafish retina with Id2aMM morpholino treatment replicate 1		Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.		tissue:retina\|genotype/variation:control	GSM949494	GSM949494: Zebrafish retina with Id2aMM morpholino treatment replicate 1; Danio rerio; RNA Seq	GSM949494 2	GSM949494: Zebrafish retina with Id2aMM morpholino treatment replicate 1	1		GEO Accession:GSM949494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP013815			Uribe201204_ctrl1.untie_1.fastq.gz	fastq	9965568192.0	49334496.0	GSM949494 r1	0:101 1:101	A:2748582966;C:2261528563;G:2269950332;T:2685506331;N:0	101	101			2748582966	2261528563	2269950332	2685506331	0	SRX155008	SRS346294	SRA054377	GEO	Department of Biomedical Engineering, Ulsan National Institute of Science and Technology	2	0.86051	0.86328	0.11721	0.11892	0.74184	0.74075	0.47603	0.47166	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		South Korea	2012-06-18	Hatching	Embryo	Eye	Sensory System