run_metadata: 41108

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
41108	SRR3679540	SRX1852527	SRS1509708	SRP076704	PRJNA326068	The transcription factor Nuclear factor erythoid 2 Nfe2 is a regulator of the oxidative stress response during Danio rerio development	GSE83466	Transcriptome Analysis	Development is a complex and well defined process characterized by rapid cell proliferation and apoptosis. At this stage in life a developmentally young organism is more sensitive to toxicants and other stressors when compared to an adult. In response to pro oxidant exposure members of the Cap’n’Collar CNC basic leucine zipper b ZIP transcription factor family including the Nfe2 related factors Nrfs activate the expression of genes that contribute to reduced toxicity. Here we studied the role of the Nrf protein Nfe2 in the developmental response to pro oxidant exposure in the zebrafish. Following acute waterborne exposures to diquat or tert buytlhydroperoxide tBOOH at three developmental stages wildtype WT and nfe2 knockout KO embryos and larvae were morphologically scored and their transcriptomes sequenced. Overall design: Wildtype animals were on the AB background and an additional germline nfe2 knockout strain were created by disruption of the nfe2 reading frame. Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hpf 48hpf and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment 20µM diquat or 1mM tBOOH for a 4 hour dosing period. Total RNA was isolated from pooled animals and 50 bp paired end libraries were sequenced using the Illumina HiSeq 2000 platform with approximately 25 million reads per sample. Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 and raw counts data normalized using DESeq2. Gene annotation was from Ensemble for GRCz10.		pubmed:27716579		96 hpf AB Diquat rep 2	GSM2203905		tissue:30 pooled zebrafish wildtype embryos AB background exposed to 20 μM Diquat. RNA sampled at 96 hpf.\|developmental stage:embryo\|genotype:wildtype	96 hpf AB Diquat rep 2	Raw RNA Sequencing RNA Seq reads were obtained from HudsonAlpha as 50bp paired end reads in FASTQ format with approximately 25 million reads per sample. Reads were analyzed for various quality control parameters including: per base sequence quality per sequence GC content sequence length distribution and sequence duplication levels and Kmer content using the FastQC tool Version 0.11.4. Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 Version 2.0.14 which functions based on Bowtie2 alignment software Version 2.2.5 using a mean inner distance of 300 bp a maximum intron length of 380 000bp and all other parameters set to default values. Read counts for each gene were then obtained for the aligned reads using the Htseq counts tool Version 0.6.1. The Tophat accepted hits BAM file was analyzed against the Ensembl GTF zebrafish gene annotation reference with pre sorting by name through Samtools Sort Samtools version 0.1.19 within the Htseq count software. Raw counts data obtained from Htseq counts were normalized using DESeq2 Version 1.10.1 in R version 3.2.3 64bit platform using size factors obtained from the total dataset and virtual reference sample based on the data. Genome build: GRCz10 Supplementary files format and content: EXCEL DeSeq2 normalized counts	30 pooled zebrafish wildtype embryos AB background exposed to 20 μM Diquat. RNA sampled at 96 hpf.	Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hpf 48hpf and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment 20µM diquat or 1mM tBOOH for a 4 hour dosing period in glass scintillation vials in a 20mL volume of 0.3x Danieau’s. For phenotypic analysis animals were moved to 0.3x Danieau’s for 48 hours post exposure hpe and imaged with a Leica M165 FC stereoscope and DFC310FX camera. For RNA Seq experiments animals were moved to 0.3x Danieau’s for 4 hpe before being flash frozen using liquid nitrogen and stored at 80°C.	Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit BioRad Hercules California USA following the manufacturer’s protocol. At HudsonAlpha Institute for Biotechnology Huntsville AL USA the quality of the RNA was checked using Caliper Instrumentation PerkinElmer Waltham MA USA and RiboGreen reagents Invitrogen Carlsbad CA USA. Directional mRNA libraries with polyA selection were made using New England Biolabs Ipswich MA USA reagents: NEBNext Poly A mRNA Isolation Magnetic Module NEBNext First Strand Synthesis Module NEBNext Second Strand Synthesis Module with dUTP NEBNext End Repair Module NEBNext dA Tailing Module and the NEBNext Quick Ligation Module. Quality analysis of the libraries was carried out using PicoGreen Thermo Fisher Waltham MA USA and Caliper instrumentation PerkinElmer Waltham MA USA. 50 base pair bp paired end libraries were sequenced using the Illumina HiSeq v4 platform at HudsonAlpha Institute for Biotechnology Huntsville AL USA.	Adults were held in 2:1 female to male groups at a density of ≤ 5 fish/l in aerated filtered and re circulated system water 28.5 °C and fertilized eggs were obtained from multiple group breedings. Wildtype animals were on the AB background Zebrafish International Resource Center Eugene OR. Fish husbandry protocols were approved by the Bates College Institutional Animal Care and Use Committee Animal Welfare Assurance Number Number A3320 01 and the University of Michigan Institutional Animal Care and Use Committee Animal Welfare Assurance Number Number A3114 01. To create a germline nfe2 knockout a pair of vectors containing TAL effector nucleases TALENs targeting exon 3 of nfe2 were generated using the REAL Restriction Enzyme And Ligation assembly method. Component plasmids were obtained from Addgene www.addgene.org/talengineering/talenkit/. Briefly target sites were selected and TALENs designed using Zifit http://zifit.partners.org/ZiFiT/ followed by assembly. mRNA was synthesized from the vectors and injected into single cell zebrafish embryos on an AB/TL hybrid background Shavit et al in preparation. The TALEN target sequences are: five prime TCACCCACCTCTTATGAG three prime and five prime CATGACTACACGTGGTCA three prime. A subsequent founder deletion of eight base pairs GCACATGA was found via sequencing in exon three starting at nucleotide position 468 from the translational start site; this deletion resulted in a frame shift causing a change in protein sequence starting at amino acid 111 M→ D and the introduction of a premature stop codon 13 amino acids later. The frameshift was introduced 161 amino acids prior to the Cap'n'collar CNC family basic leucine zipper domain that is responsible for DNA binding.	developmental stage:embryo\|genotype:wildtype	GSM2203905	GSM2203905: 96 hpf AB Diquat rep 2; Danio rerio; RNA Seq	GSM2203905		1	Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit BioRad Hercules California USA following the manufacturer’s protocol. At HudsonAlpha Institute for Biotechnology Huntsville AL USA the quality of the RNA was checked using Caliper Instrumentation PerkinElmer Waltham MA USA and RiboGreen reagents Invitrogen Carlsbad CA USA. Directional mRNA libraries with polyA selection were made using New England Biolabs Ipswich MA USA reagents: NEBNext Poly A mRNA Isolation Magnetic Module NEBNext First Strand Synthesis Module NEBNext Second Strand Synthesis Module with dUTP NEBNext End Repair Module NEBNext dA Tailing Module and the NEBNext Quick Ligation Module. Quality analysis of the libraries was carried out using PicoGreen Thermo Fisher Waltham MA USA and Caliper instrumentation PerkinElmer Waltham MA USA. 50 base pair bp paired end libraries were sequenced using the Illumina HiSeq v4 platform at HudsonAlpha Institute for Biotechnology Huntsville AL USA.	GEO Accession:GSM2203905	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP076704			96_AB_diquat_2_fwd.fastq.gz 96_AB_diquat_2_rev.fastq.gz	fastq fastq	2922210900.0	29222109.0	GSM2203905 r1	0:50 1:50	A:787614443;C:668655271;G:673472999;T:790874783;N:1593404	50	50			787614443	668655271	673472999	790874783	1593404	SRX1852527	SRS1509708	SRA434415	GEO	Biochemistry & Biomedical Sciences, McMaster University	2	0.94396	0.94807	0.1044	0.10356	0.65924	0.66066	0.48276	0.48013	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown		Canada	2016-06-17	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures