{"database": "metadata", "table": "run_metadata", "rows": [[41118, "SRR3679530", "SRX1852517", "SRS1509698", "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\u2019n\u2019Collar 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  20\u00b5M 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.", null, "pubmed:27716579", null, "48 hpf Nfe2 KO Diquat rep 1", "GSM2203895", null, "tissue:30 pooled zebrafish Nfe2 knock out embryos AB background  exposed to 20 \u03bcM Diquat. RNA sampled at 48 hpf.|developmental stage:embryo|genotype:Nfe2 knock out", "48 hpf Nfe2 KO Diquat rep 1", "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 Nfe2 knock out embryos AB background  exposed to 20 \u03bcM Diquat. RNA sampled at 48 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  20\u00b5M diquat or 1mM tBOOH for a 4 hour dosing period in glass scintillation vials in a 20mL volume of 0.3x Danieau\u2019s. For phenotypic analysis  animals were moved to 0.3x Danieau\u2019s 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\u2019s for 4 hpe before being flash frozen using liquid nitrogen and stored at  80\u00b0C.", "Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit BioRad  Hercules  California  USA following the manufacturer\u2019s 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 \u2264 5 fish/l in aerated  filtered  and re circulated system water 28.5 \u00b0C 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\u2192 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:Nfe2 knock out", "GSM2203895", "GSM2203895: 48 hpf Nfe2 KO Diquat rep 1; Danio rerio; RNA Seq", "GSM2203895", null, "1", "Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit BioRad  Hercules  California  USA following the manufacturer\u2019s 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:GSM2203895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP076704", null, null, "48_Nfe2KO_diquat_1_fwd.fastq.gz 48_Nfe2KO_diquat_1_rev.fastq.gz", "fastq fastq", 2777659000.0, 27776590.0, "GSM2203895 r1", "0:50 1:50", "A:747538012;C:636325899;G:642869083;T:749460590;N:1465416", 50, 50, null, null, 747538012, 636325899, 642869083, 749460590, 1465416, "SRX1852517", "SRS1509698", "SRA434415", "GEO", "Biochemistry & Biomedical Sciences, McMaster University", 2, 0.94578, 0.95075, 0.10123, 0.10065, 0.69045, 0.69029, 0.45626, 0.46782, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2016-06-17", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["41118"], "units": {}, "query_ms": 9.044475998962298}