Transcription profiling by high throughput sequencing of zebra fish tissues and developmental stages
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ABSTRACT:
ORGANISM(S): Danio rerio
SUBMITTER: John Collins
PROVIDER: E-MTAB-434 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Abstract: As part of the zebrafish genome annotation project the 3 prime ends of genes were pulled down on polyT beads and sequenced on the Illumina Genome Analyzer to identify alternative 3 prime ends in a range of tissues and developmental stages. <br> Study description: Total RNA from a range of developmental stages and adult tissues were chemically fragmented, pulled down on polyT magnetic beads and double stranded cDNA was synthesized. The cDNA was BpmI digested to release from the beads and to leave a 6 T base tail. Illumina sequencing libraries were made followed by 76 base paired-end sequencing.
2011-07-01 | E-MTAB-308 | biostudies-arrayexpress
Project description:Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer.
2011-01-28 | E-MTAB-460 | biostudies-arrayexpress
Project description:Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages using the Illumina Genome Analyzer Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues and developmental stages using the Illumina Genome Analyzer. These data have been used to improve the gene annotation of the zebrafish genome. Study description: Zebrafish total RNA was extracted from embryonic and adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 36, 37, 54 and 76 base reads on the Illumina Genome Analyzer. ArrayExpress Release Date: 2011-03-11 Person Roles: submitter Person Last Name: Collins Person First Name: John Person Mid Initials: E Person Email: jec@sanger.ac.uk Person Phone: 01233 834244 Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30603 | GEO
Project description:Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer. ArrayExpress Release Date: 2011-01-28 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
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Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in freeze-dried whole sediment samples and their corresponding organic extracts in parallel. To this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerable extent be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Additionally, different gene expression was shown to be less influenced by the sampling site than by the method of exposure, which could be attributed to differential bioavailability of contaminants. Microarray analyses were performed with early life stages of zebrafish exposed to sediment extracts or freeze-dried sediment from three sampling sites (Ehingen, Lauchert, Sigmaringen) along the Upper part of the Danube River, Germany. The expression profiles were compared within the sampling sites, between the exposure scheme and to the expression pattern of model toxicants, such as 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, mechanism-specific bioassays and chemical analysis of the sediments have been combined and compared to the present gene expression data.
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2014-10-15 | E-GEOD-51890 | biostudies-arrayexpress
Project description:RNA-seq was performed to reveal the RNA expression profile at two different stages (shield and tail-bud stage) in the embryogenesis of zebrafish (wild type strain AB). Zebrafish embryos were collected at the shield stage and tail-bud stage, which correspond to 6 hours post fertilization (hpf) and 10 hpf, respectively. Total RNA was extracted with miRNeasy Mini Kit, libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit (Illumina), and paired-end sequencing was performed using NovaSeq 6000 (Illumina).
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Project description:Total RNA was extracted from adult male and female zebrafish. Illumina cDNA libraries were prepared from polyA+ RNA and sequenced using Illumina HiSeq paired-end sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ protocol: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Libraries were made using the Illumina cDNA protocol from polyA+ RNA.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
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