Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq analysis of single bovine blastocysts

ABSTRACT: Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology RNA was extracted from individual D7 bovine blastocysts (Arcturus Picopure), cDNA was synthesized and amplified (Nugen Ovation) and indexed libraries were created for sequencing (Nugen Encore)

ORGANISM(S): Bos taurus

SUBMITTER: James Chitwood

PROVIDER: E-GEOD-44023 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

RNA-seq analysis of single bovine blastocysts.

Chitwood James L JL Rincon Gonzalo G Kaiser German G GG Medrano Juan F JF Ross Pablo J PJ

BMC genomics 20130525

<h4>Background</h4>Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect.<h4>Results</h4>We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detect ...[more]

PMID: 23705625

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Project description:Embryo transfer is largely used in cattle and classically performed at D7 (or D8) using unsorted D7 (or D8) blastocysts produced in vivo, or in vitro in defined media without serum or feeders. Outdated systems including serum and co-culture were however of interest for research purposes. We thus wondered whether embryos that would form a blastocoel at different times after fertilisation (D6 to D8) and stay in culture for up to 2 additional days (D6+1, D6+2, D7+1) would equally develop in vivo after temporary transfer to oestrus-synchronised recipients. Globally alike, those that survived up to D18 reached primitive streak stages and elongated to filamentous sizes similarly to in vivo (D18) or in vitro controls (classical D7-T7). Recovery rate differed between D6 and D8 embryos that were immediately transferred (58 vs 25% in D6-T6 vs D8-T8). With a reduced but intermediate survival (33%), the D6 embryos that stayed 2 more days in culture produced 7 times more IFN-tau at D18 than the immediately transferred D6 embryos. At the end of the culture, D6+2 embryos also displayed the higher number of differences with the D6 blastocysts. A “+1” phenotype emerged from the D6+1 and D7+1 embryos, that shared a larger gene set enrichment than the blastocysts they derived from, possible sign of a similar adaption to the in vitro environment. To the best of our knowledge, this is the first time that this culture system (B2, serum, co-culture) is used to study its impacts on the embryonic transcriptome prior to transfer. Initially reputed as beneficial to produce more expanding and hatching blastocysts, this culture system generated blastocysts that all dissembled in vivo developed ones (D7). Despite a loss of 40 to 60% in the two weeks after ET, no dying (vs surviving) signature was detectable in any of the transferred groups (D6, D6+2, D7+1, D8); was it rather a matter of developmental “pause”? Whether molecular differences prevailing to transfer partly reflected those induced by unfavourable conditions (or diapause) was therefore assessed.

Dataset Information

RNA-seq analysis of single bovine blastocysts

Publications

RNA-seq analysis of single bovine blastocysts.

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