run_metadata: 38234
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 |
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| 38234 | SRR1565814 | SRX692866 | SRS694592 | SRP046222 | PRJNA260259 | Neurotranscriptome profiles of four zebrafish strains | GSE61108 | Transcriptome Analysis | Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays | pubmed:25326170;pubmed:26032017;pubmed:26309813 | LSB female rep2 | GSM1496854 | tissue:whole brain|strain:Low Stationary Behavior|Sex:female|age:17 weeks | LSB female rep2 | Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using "union" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample | whole brain | Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA | strain:Low Stationary Behavior|Sex:female|age:17 weeks | GSM1496854 | GSM1496854: LSB female rep2; Danio rerio; RNA Seq | GSM1496854 | 1 | Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA | GEO Accession:GSM1496854 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP046222 | lsbf2.combined.fastq | fastq | 3396163712.0 | 49943584.0 | GSM1496854 r1 | 0:68 | A:952427292;C:755558175;G:739625271;T:948206206;N:346768 | 68 | 952427292 | 755558175 | 739625271 | 948206206 | 346768 | SRX692866 | SRS694592 | SRA181596 | GEO | Biology, University of Nebraska at Omaha | 1 | 0.91971 | 0.09762 | 0.7139 | 0.53907 | 68 | B | usable mapping rate | illumina | early_illumina | full_length | random_priming | trueseq | bulk | unknown | unknown | United States | 2014-09-04 | Adult | Adult | Brain | Nervous System |