Transcription profiling by array of lymphoblastic cells, fat and skin from twins
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Alexandra Nica
PROVIDER: E-MTAB-522 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Epigenetic changes such as DNA methylation variation are known to play a role in gene regulation and common disease susceptibility. Little is known about the genome-wide frequency, localization and function of such changes and how they are regulated by genetic and environmental factors. We have utilized the MuTHER resource and generated methylation profiles across multiple tissues conducted in a large set of female individuals that allows systematic dissection of genetic and non-genetic effects on DNA methylation. DNA methylation was quantified in subcutaneous fat and skin derived from 648 TwinsUK participants using the Infinium HumanMethylation450 BeadChips. Data from transcription profiling of skin, adipose fat and lymphoblastoid cell lines (LCLs) from the same set of TwinsUK participants have been deposited in ArrayExpress under accession number E-TABM-1140 (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-1140).
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Project description:Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression. Methods: ampulla and isthmus samples of animals with a large pre-ovulatory follicle and a large CL (LF/LCL) and animals with a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms. Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively. Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility. Oviductal mRNA profiles of cows with different endocrine milleus were generated by next generation sequencing.
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