run_metadata: 55377

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
55377	SRR10322137	SRX7032948	SRS5553008	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.		pubmed:35504924		mCherry control RNA seq #2	GSM4134347		tissue:lck mCherry\|genotype/variation:control	mCherry control RNA seq #2	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck mCherry	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:control	GSM4134347	GSM4134347: mCherry control RNA seq #2; Danio rerio; RNA Seq	GSM4134347		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134347	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP226571			Lck_mch_2_1.fastq.gz Lck_mch_2_2.fastq.gz	fastq fastq	8556568306.0	85629202.0	GSM4134347 r1	0:99.93 1:99.93	A:2299427498;C:1945648999;G:1981590842;T:2329900967;N:0	99	99			2299427498	1945648999	1981590842	2329900967	0	SRX7032948	SRS5553008	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94792		0.25274		0.80085		0.51772		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system