Transcriptome profiling of mutant embryos from the Mouse Genetics Project DMDD
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Mus musculus
SUBMITTER:
PROVIDER: E-ERAD-272 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Total RNA was extracted from wildtype embryos of developmental stage E14.5 for baseline expression study relating to the Mouse Genetics Project (http://www.dmdd.org.uk/). Protocol: After DNase treatment, fragmented RNA was enriched for the 3 ends by pull down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 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 2 at the 5 end followed by 10 bases HBDVHBDVHB (using the single base code), then one of 96 eight base indexing tags, 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 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/
2014-04-28 | E-ERAD-243 | biostudies-arrayexpress
Project description:Total RNA was extracted from dissected muscle from tert homozygous and wild type adult zebrafish. 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/
2016-05-03 | E-ERAD-456 | biostudies-arrayexpress
Project description:Establish a baseline expression transcriptional signatures for zebrafish developmenal stages. Total RNA was extracted from pools of wild type zebrafish embryo at a series of different developmental stages in replicate. The 3 end of fragmented RNA was pulled down using a 30T polyT oligo 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 embryo pools and DNase treated. Fragmented RNA was enriched for the 3 ends by pulled down using an anchored 30 T polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 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 2 at the 5 end followed by the 10 bases HBDVHBDVHB, then one of 96 eight base indexing tags, 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 morphologically abnormal and wildtype sibling larvae of neural crest mutants derived from ENU mutagenesis. Total RNA was extracted from zebrafish embryos and DNase treated. Fragmented RNA was enriched for the 3 ends by pulled down using a 30T polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 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 2 at the 5 end followed by 10 bases HBDVHBDVHB, then one of 96 eight base indexing tags, 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/
2014-07-23 | E-ERAD-275 | biostudies-arrayexpress
Project description:Total RNA was extracted from mutant and wildtype sibling larvae of muscle mutants derived from ENU mutagenesis. Total RNA was extracted from zebrafish embryos and DNase treated. Fragmented RNA was enriched for the 3 ends by pulled down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 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 2 at the 5 end followed by 10 bases HBDVHBDVHB, then one of 96 eight base indexing tags, 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/
2014-09-09 | E-ERAD-281 | biostudies-arrayexpress
Project description:Total RNA was extracted from embryonic lethal homozygous gene knockout and sibling embryos from the Mouse Genetics Project (http://www.dmdd.org.uk/). 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 mouse embryos and DNase treated. 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 polyToligo with part of Illumina adapter 1 at the 5 end followed by 4 random bases, then an A, C or G base, then one of twelve 5 base indexing tags and 14 T bases. An Illumina library with full adapter sequence was produced by 15 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/
2014-04-28 | E-ERAD-237 | biostudies-arrayexpress
Project description:Total RNA was extracted from zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project (http://www.sanger.ac.uk/Projects/D_rerio/zmp/). 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/
2014-10-15 | E-ERAD-305 | biostudies-arrayexpress
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/
2015-01-20 | E-ERAD-323 | biostudies-arrayexpress
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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