EQTL Mapping of Mid-Secretory Phase Endometrial Cells
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ABSTRACT:
PROVIDER: PRJNA325331 | ENA |
REPOSITORIES: ENA
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Project description:<p>We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle. Biopsies were collected from 58 women with two or more early pregnancy losses and 53 of these samples passed all quality control. RNA was extracted from endometrial biopsies and DNA was extracted for sequencing from blood.</p> <p>Gene expression data can be found at NCBI GEO Series GSE77688.</p>
| phs001146 | dbGaP
Project description:We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium.
2016-02-09 | GSE77688 | GEO
Project description:Fertility traits in humans are heritable, however, little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals, particularly women. To address this gap in knowledge, we performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium. We identified 423 cis-eQTLs for 132 genes that were significant at a false discovery rate (FDR) of 1%. After pruning for strong LD (r2 >0.95), we tested for associations between eSNPs and fecundability, measured as the length of the interval to pregnancy, in 117 women. Two eSNPs were associated with fecundability at a FDR of 5%; both were in the HLA region and were eQTLs for the TAP2 gene (P = 1.3x10-4) and the HLA-F gene (P = 4.0x10-4), respectively. The effects of these SNPs on fecundability were replicated in an independent sample. The two eSNPs reside within or near regulatory elements in decidualized human endometrial stromal cells. Our study integrating eQTL mapping in a primary tissue with association studies of a related phenotype revealed novel genes and associated alleles with independent effects on fecundability, and identified a central role for two HLA region genes in human implantation success. 53 women underwent endometrial biopsies as part of their clinical evaluation for recurrent pregnancy loss, after obtaining informed consent. These women were between the ages of 26 and 43 years and had at least two previous pregnancy losses before10 weeks gestation.
2016-02-09 | E-GEOD-77688 | biostudies-arrayexpress
Project description:Study question: Does a comprehensive study involving two different population cohorts and small RNA sequencing from endometrium and blood reveal new endometrial receptivity-related microRNAs (miRNAs) in healthy conditions and in women with recurrent implantation failure (RIF)? Summary answer: Several annotated miRNAs, not previously associated with endometrial receptivity, as well as one novel miRNA were found as differentially expressed between early secretory vs. mid-secretory phase samples in addition to miRNAs dysregulated in RIF patients. What is known already: The involvement of miRNAs in mid-secretory endometrial functions has been shown and aberrant expression of miRNAs in RIF has been identified in a few previous studies, but not from whole blood samples. However, as the analysis settings and platforms have been different and a small number of samples has been analysed, there is no consensus about the miRNAs involved in endometrial receptivity and dysfunction. Participants/materials, setting, methods: A total of 116 endometrial and 114 blood samples were subjected to Illumina small RNA sequencing. Identification of annotated and novel miRNAs from sequencing reads was performed by miRDeep2 algorithm. miRNAs that had significantly altered levels between the study groups in both EST and ESP datasets were considered as differentially expressed. Ingenuity Pathway Analysis was applied for identifying miRNA target genes and respective canonical pathways from the matched mRNA analysis from the same samples. Custom TaqMan Small RNA assay was used for the validation of novel miRNA (chr2_4401) levels from paired early secretory and mid-secretory endometrial samples. Main results and the role of chance: Among fertile women, 91 differentially expressed miRNAs were identified in mid-secretory vs. early secretory endometrium, while no differentially expressed miRNAs were found in the corresponding blood samples. The comparison of mid-secretory phase samples between fertile women and RIF patients revealed 21 differentially expressed miRNAs from endometrium and one from blood samples. miRNA target gene prediction analysis using our mRNA sequencing data from the matched samples detected several canonical pathways to be involved in mid-secretory endometrial functions, including JAK/STAT signalling, leptin signalling and growth hormone signalling. Moreover, JAK/STAT signalling pathway was also revealed in miRNA target analysis of mid-secretory endometrium from RIF patients when compared to fertile women. Further, our study results highlight the involvement of miR-30 and miR-200 families in endometrial receptivity, and miR-424-5p in the development of endometrial dysfunction. We identified several novel miRNAs, of which miRNA chr2_4401, being 37-fold up-regulated in mid-secretory phase, has a potential role in the mid-secretory endometrial functions. From blood samples we identified miR-30a-5p as a possible marker of infertility related to RIF.
2019-07-18 | GSE108966 | GEO
Project description:Purpose- To identify the pathways and processes that are dysregulated in the eutopic endometrium of women with endometriosis Methods-RNA sequencing was used to detect and quantify the transcripts encoded by the whole genome in the eutopic endometrium. Mid-secretory phase eutopic endometrial samples from women with (n=4) and without endometriosis (n=4) were processed for RNA sequencing and the data were compared to identify the transcripts displaying differential abundance in women with endometriosis, compared to those without endometriosis (controls)
2021-03-28 | GSE153740 | GEO
Project description:Transcriptional profiling of the mid-secretory phase eutopic endometrial samples from women with endometriosis
| PRJNA643840 | ENA
Project description:We present the transcriptome analysis by RNA sequencing of endometrial B cells identifying potential B cell phenotypes and function in human endometrium during the mid-luteal phase. To achieve this, endometrial B cells were isolated from 15 endometrial biopsies, and cDNA library preparation was performed for RNA sequencing.
2021-07-24 | GSE180728 | GEO
Project description:To identify differentially expressed transcripts (long-noncoding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) and competing endogenous RNA (ceRNA) networks closely connected with endometrial receptivity, we analyzed gene expression profiles between the proliferative and mid-secretory endometria in fertile women.
2021-02-24 | GSE167325 | GEO
Project description:Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital for embryo implantation. As the footrace for universal endometrial receptivity markers continues, RNA-seq remains the most powerful tool for transcriptomic marker discovery. In this study, we aimed to elucidate endometrial maturation mechanisms at transcriptomic level and identify novel robust biomarker candidates for endometrial receptivity in a multicentre study. Additionally, we compared mid-secretory transcriptome profiles from healthy women with profiles of women with repeated IVF failure to find transcriptome changes related to problems with endometrial receptivity.
2020-11-07 | GSE106602 | GEO
Project description:eQTL Mapping of Mid-Secretory Phase Endometrial Cells
| PRJNA325332 | ENA