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Whole genome bisulfite sequencing of bovine oocytes from metabolically divergent lactating cows and nulliparous heifers

ABSTRACT: Whole genome bisulfite sequencing of bovine oocytes from metabolically divergent lactating cows and nulliparous heifers

PROVIDER: PRJEB33720 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3454170.fastq.gz	Fastqsanger.gz
	ERR3454180.fastq.gz	Fastqsanger.gz
	ERR3454190.fastq.gz	Fastqsanger.gz
	ERR3454200.fastq.gz	Fastqsanger.gz
	ERR3454210.fastq.gz	Fastqsanger.gz

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Whole genome bisulfite sequencing of bovine oocytes from metabolically divergent lactating cows and nulliparous heifers

Project description:Lactating cows experience transient metabolic stresses during postpartum which results in abnormal concentrations of non-esterified fatty acids and beta-hydroxybutyrate that can impact oocyte maturation and ultimately reproductive success. We hypothesize that metabolic challenges in lactating cows influence DNA methylation changes of the oocyte affecting genes involved in oocyte developmental competency. Therefore, we compared whole genome bisultfite sequencing (wgbs) of the oocytes collected from 5-6 week (early) or 9-10 week (mid) post-partum against that of oocytes from nulliparous heifers as metabolically unchallenged condition control. Bisulfite-Seq DNA libraries were generated from pooled oocytes using an EZ DNA methylation-direct kit and Pico-Methyl seq library preparation kit (Zymo Research), and parallel sequenced using the illumina HiSeq2500 system.

2021-11-30 | E-MTAB-8191 | biostudies-arrayexpress

Whole genome bisulfite sequencing of bovine morula derived from metabolically divergent dairy cows

Project description:Lactating cows experience transient metabolic stresses during postpartum which results in abnormal concentrations of non-esterified fatty acids and beta-hydroxybutyrate that can affect embryo-maternal communication and ultimately reproductive success. We hypothesize that metabolic challenges in lactating cows influence DNA methylation changes of the embryos prior to implantation affecting genes involved in embryo developmental competency. Therefore, we compared whole genome bisulfite sequencing (wgbs) of morulas derived from in vitro produced 2-4 cell embryos and transferred in the oviduct of metabolically profiled lactating cows until day 7. Similar stage of in vitro production (IVP) embryos were transferred to the oviduct of nulliparous heifers as a metabolically unchallenged control. Bisulfite-Seq DNA libraries were generated from groups of five morulas using an EZ DNA methylation-direct kit and Pico-Methyl seq library preparation kit (Zymo Research), and parallel sequenced using the illumine HiSeq2500 system at the institute of Genome Biology, Leibniz-Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.

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Gene expression profile at single cell level of intestinal lamina propria cells from nulliparous mice and lactating mice

Project description:We used single cell RNA sequencing (scRNA-seq) to analyze the differentially expressied genes in lamina propria cells and compare them between nulliparous mice and lactating mice.

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Gene expression in extra-embryonic tissues flushed out at D18 from heifers, early and late lactating cows

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Gene expression in extra-embryonic tissues flushed out at D18 from heifers, early and late lactating cows

Project description:Evaluate the influence of maternal metabolism on gene expression profiles from extra-embryonic tissues at D18 Keyword: Holstein Heifers and Postpartum dairy cows, metabolism and energy status, elongation and gastrulation, extra-embryonic tissues, transcriptome, correlations between genes & metabolites? 8 replicates in GH, 11 replicates in ELC and 10 replicates in LLC (extra-embryonic tissues) per group of female (N=3) were hybridized (total N=29) against a placental reference that hybridized itself to 99% of the array. Hybridization design: 6 microarrays per experiment (N=5) were randomly hybridized to the EET from 2 conceptuses originating either from development in heifers, ELC or LLC. Extra-embryonic tissues were systematically labelled with Cy3 and Reference in Cy5.

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RNA-seq profiling of theca and granulosa tissue of dominant follicle at 3 stages of follicular development in cows and heifers.

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Consequences of supplying methyl donors during pregnancy on the methylome of the offspring from lactating and non-lactating dairy cattle

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Faecal samples from lactating dairy cows

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