EGAS00001000098-sc-2019-08-21T10:35:07Z - samples
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ABSTRACT:
PROVIDER: EGAD00001005274 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, subjected to Chromatin Immunoprecipitation using an antibody for H3K4me1. H3K4me1 peaks mark distal regulatory elements.
| EGAS00001000098 | EGA
Project description:50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, processed with the FAIRE assay in order to generate maps of open chromatin. .
This dataset contains all the data available for this study on 2019-08-21.
| EGAD00001005273 | EGA
Project description:50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, processed with the FAIRE assay in order to generate maps of open chromatin.
| EGAS00001000097 | EGA
Project description:The goal of this study is to identify likely sites of polycistronic transcription initiation in a kinetoplastid parasite. Peaks in histone H3 acetylations were found to mark these likely sites, with TBP and SNAP50 enriched upstream of these acetylation peaks. Acetylation peaks are greater in rapidly dividing cells than in stationary cells. Each ChIP sample was compared to an input chromatin sample that underwent a mock immunoprecipitation (without antiserum), or in the case of acetylH3 ChIPs, used an antiserum that recognized total H3 histones. Log ratios and raw scores for each probe are provided.
2010-05-16 | E-GEOD-13415 | biostudies-arrayexpress
Project description:Histone modifications are important markers of function and chromatin state, yet the DNA elements that direct them to specific locations in the genome are poorly understood. Here we use the genetic variation in Yoruba lymphoblastoid cell lines as a natural experiment to identify genetic differences that affect histone marks and to better understand their relationship with transcriptional regulation. Across the genome, we identified hundreds of quantitative trait loci that impact histone modification or RNA polymerase (PolII) occupancy. In many cases the same variant is associated with quantitative changes in multiple histone marks and PolII, as well as in DNaseI sensitivity and nucleosome positioning, indicating that these molecular phenotypes often share a single underlying genetic cause. Variants that impact chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters; while most of these distal regulators enhance promoter activity, some act as distal chromatin silencers. Finally, we find that polymorphisms in transcription factor binding sites are often causally responsible for variation in local histone modification. In summary, the class of variants identified here generate coordinated changes in chromatin both locally and sometimes at distant locations, frequently drive changes in gene expression, and likely play an important role in the genetics of complex traits. ChIP-seq of RNA Polymerase II and 4 histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3) in 10 unrelated Yoruba HapMap lymphoblastoid cell lines
2013-10-01 | E-GEOD-47991 | biostudies-arrayexpress
Project description:By performing methylated RNA immunoprecipitation sequencing (MeRIP-seq) to profile a transcriptome-wide N6-methyladenine modification in lymphoblastoid cell lines (LCLs) of 18 individuals from 6 YRI families. We found that that more than 70% of m6A peaks are shared by children and their parents, but the difference between patients and children is higher than that between families. The group-specific peaks in children are primarily enriched in cell cycle control, while those in parents are mainly enriched in chromatin/histone modifications. Moreover, the protein-protein interaction(PPI) network showed that seven significantly m6A regulators were closely interact with age-related genes, APOE and CEBPA, . In addition, we found that more SNPs are enriched around m6A peaks, and both parents-derived SNVs and de novo mutations could contribute to m6A methylation levels.
2023-11-18 | GSE222420 | GEO
Project description:Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci responsible for normal-range intelligence. We conducted array-based genome-wide gene expression analysis aiming to identify genes displaying significant difference among monozygotic twin pairs manifesting between-co-twins IQ differences. Total RNA was isolated from B-lymphoblastoid cell lines and applied to Affymetirx arrays after reverse transcription. 17 twin pairs (34 subjects) were recruited in this study.
2012-10-20 | E-GEOD-33476 | biostudies-arrayexpress
Project description:Established dogma holds that all facets of chromatin organization and histone posttranslational modification are complete before sperm exits the testes. Using proteomic analysis to contrast immature spermatozoa and mature sperm from the epididymis, we find progressive changes in multiple histone posttranslational modifications, including H3K4me1, H3K27ac H3K79me2, H3K64ac, H3K122ac, H4K16ac, H3K9me2, and H4K20me3. In contrast, levels of H3K4me3 and H3K27me3 remained constant. Using chromatin immunoprecipitation coupled with deep sequencing, we find that changes in H3K27ac and H3K9me2 involve sharpening broad diffuse regions into narrow peaks, centered on promoters and distal enhancers driving embryonic development (H3K27ac) or tissue-specific genes sequestered in lamina-associated domains (H3K9me2). Maturing sperm contain the histone deacetylase enzymes HDAC1 and HDAC3, suggesting the NuRD complex may drive these changes. These data extend our understanding of germline programming and reveal that, in addition to trafficking noncoding RNAs, alterations to histone structure are a core feature of epididymal maturation.
2022-01-01 | GSE185603 | GEO
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).
2013-10-01 | E-MTAB-1866 | biostudies-arrayexpress
Project description:Chromatins were prepared from myeloid progenitor cell line Tot2 cells transduced with retrovirus for control MSCV or MSCV-IRF8. Chromatin immunoprecipitation (ChIP) was carried out by using anti-IRF8 antibody, anti-PU.1 antibody or anti-histone H3K4me1 antibody. ChIP-Seq peaks were identified using the FindPeaks tool in the HOMER package or SICER with input DNA tags as background distribution. Potential IRF8-direct target genes were identified based on ChIP-Seq and the alteration of expression by IRF8-induction.
2013-01-24 | GSE38824 | GEO