run_metadata: 43839

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
43839	SRR6170097	SRX3280946	SRS2591755	SRP119921	PRJNA414225	Differential gene expression in the liver of zebrafish larvae exposed to 1 mM inorganic arsenic from xxx 120 hpf	GSE104953	Transcriptome Analysis	The goal of this study is to compare gene expression levels in the livers of larval Tgfabp10:nls mcherry exposed to 1 mM inorganic arsenic from xxx 120 hpf to the unexposed siblings. Samples were collected from Tgfabp10:nls mcherry zebrafish larvae that were derived from incrossed parents of the same strain. The background of transgenic lines were typically from mixed outcrosses of the transgenics to AB TAB5 and TAB14 strains when regenerating the lines as the working stocks aged. All samples were collected at approximately 120 hpf natural spawning at 8:30 9:00AM EST on day zero samples were collected at 8 10AM EST on day 5. Overall design: Zebrafish larvae that were untreated control or those exposed to 1 mM inorganic arsenic from 4 hpf 120 hpf were anesthetized and the liver was microdissected from xxx 20 larvae and pooled per treatment group. The transgenic line Tgfabp10:nls mcherry was used to facilitate microdissection of the liver. RNA was extracted using the Zymo Quick RNA Micro Kit with on column DNase treatment. Libraries were prepared according to Illumina Truseq RNA sample prep kit version 2 followed by Ribo Zero Gold treatment.		pubmed:29361514		A3	GSM2810890		source name:5dpf embryos liver arsenic\|genotype/variation:Tgfabp10:nls mcherry\|developmental stage:5 dpf\|exposed to:1 mM inorganic arsenic\|tissue:liver	A3	Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and low quality sequence p 4 e 100 y a m 10 best strata Trimmed read were mapped to GRCz10 whole genome using tophat2 v2.1.0 with parameters no novel juncs G Accepted bam files were used for counting read numbers of each gene with HTSeq s no t exon i gene id Test of differential expression of each genes was implemented by DESeq2 in Bioconductor genes with reads number less than 10 were filtered out Genome build: GRCz10 https://www.ncbi.nlm.nih.gov/grc/zebrafish Supplementary files format and content: .txt file. Reads count of genes	5dpf embryos liver arsenic		10 20 livers from 5dpf embryos were pooled per sample and RNA was extracted using the Zymo Quick RNA Micro Kit with on column DNase treatment per manufacturer's instructions. RNA seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol		genotype/variation:Tgfabp10:nls mcherry\|developmental stage:5 dpf\|exposed to:1 mM inorganic arsenic\|tissue:liver	GSM2810890	GSM2810890: A3; Danio rerio; RNA Seq	GSM2810890		1	10 20 livers from 5dpf embryos were pooled per sample and RNA was extracted using the Zymo Quick RNA Micro Kit with on column DNase treatment per manufacturer's instructions. RNA seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol	GEO Accession:GSM2810890	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP119921			Sample_A3-299_read1.fastq.gz Sample_A3-299_read2.fastq.gz	fastq fastq	13287203066.0	65778233.0	GSM2810890 r1	0:101 1:101	A:3662325148;C:3087171770;G:3305939687;T:3067414232;N:164352229	101	101			3662325148	3087171770	3305939687	3067414232	164352229	SRX3280946	SRS2591755	SRA619573	GEO	Biology, New York University Abu Dhabi	2	0.92398	0.92463	0.03399	0.03434	0.79547	0.81044	0.52707	0.53016	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown		United Arab Emirates	2017-10-13	Larval	Larval	Liver	Liver and Biliary System