Genome annotation of zebrafish: identification of alternative 3 prime ends in a range of tissues and developmental stages
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ABSTRACT:
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.
ORGANISM(S): Danio rerio
SUBMITTER: John Collins
PROVIDER: E-MTAB-308 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description: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. 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. ArrayExpress Release Date: 2010-10-14 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
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Project description:Abstract: 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.
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2016-05-03 | E-ERAD-456 | biostudies-arrayexpress
Project description:Total RNA was extracted from morpholigcally abnormal and wildtype sibling larvae of neural crest mutants derived from ENU mutagenesis. The 3 end of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using Illumina HiSeq paired-end sequencing. Protocol: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. 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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Project description:Total RNA was extracted from zebrafish embryos at a range of developmental stages which were treated with small molecules at different concentrations and from their corresponding solvent treated and untreated controls. The 3' end of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted and DNase treated. Fragmented RNA was enriched for the 3 ends by pull down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. 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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Project description:Establish baseline expression transcriptional signatures for zebrafish developmental stages. Total RNA was extracted from single wild type zebrafish embryos at a series of different developmental stages. The 3' ends of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted and DNase treated. Fragmented RNA was enriched for the 3 ends by pull down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. 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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Project description:Total RNA was extracted from zebrafish embryos collected for one or more alleles of neural crest mutants. The 3' ends of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted and DNase treated. Fragmented RNA was enriched for the 3 ends by pull down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by PCR. 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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