run_metadata: 48895

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
48895	SRR7444114	SRX4314653	SRS3474413	SRP151493	PRJNA478247	Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA seq]	GSE116358	Transcriptome Analysis	The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5. Overall design: For RNA seq gene expression was compared in whole two wpf zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA Seq analysis in three wpf zebrafish larvae that were WT mda5mk29/mk29 zbtb24mk22/mk22 and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype. For ERRBS DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.	parent bioproject:PRJNA478246	pubmed:30484769		WT2A	GSM3229930		tissue:Fin\|development stage:Larvae\|genotype/variation:WT	WT2A	Reads were mapped to the Zebrafish genome danRer7 using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engström et.al Nat. Meth. 2013. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done on the second pass the RemoveNoncanoncial flag was used. Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq. Genome build: danRer7 Supplementary files format and content: Tab delimited normalized RNA seq counts per million for each sample.	Fin		Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run using the TruSeq SBS v4 Kit Illumina.		development stage:Larvae\|genotype/variation:WT	GSM3229930	GSM3229930: WT2A; Danio rerio; RNA Seq	GSM3229930		1	Total RNA was isolated using Trizol Invitrogen and precipitated with isopropanol. post RiboGreen quantification and quality control by Agilent BioAnalyzer 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina TruSeq Stranded mRNA LT Kit with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run using the TruSeq SBS v4 Kit Illumina.	GEO Accession:GSM3229930	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP151493			WT_2A_IGO_06387_3_S71_L008_R1_001.fastq.gz WT_2A_IGO_06387_3_S71_L008_R2_001.fastq.gz	fastq fastq	3402949100.0	34029491.0	GSM3229930 r1	0:50 1:50	A:891664443;C:800386138;G:792288516;T:909424992;N:9185011	50	50			891664443	800386138	792288516	909424992	9185011	SRX4314653	SRS3474413	SRA729908	GEO	Center for Pharmacogenomics, Washington University School of Medicine	2	0.95927	0.96093	0.10072	0.10101	0.65717	0.6604	0.48926	0.49224	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		United States	2018-06-27	Larval	Larval	Fin	Surface Structure