Single-cell replication timing analysis of hTERT-RPE1 cells depleted for SAF-A protein
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 1500
ORGANISM(S): Homo sapiens
SUBMITTER: Shin-ichiro Hiraga
PROVIDER: E-MTAB-10234 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study was undertaken to identify novel tumour suppressor genes in lung adenocarcinoma. EYA4, located at 6q23.2 was identified as a frequently lost and hypermethylated gene in the analyzed samples. 7 Breast cancer cell lines profiled on the SMRTr array in conjunction with matched DNA methylation data, allelic status and gene expression data for integrative analysis.
2010-12-31 | E-GEOD-21540 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE17768: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: gene expression GSE17769: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: DNA methylation GSE21347: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status GSE21540: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: CGH Refer to individual Series
2010-12-31 | E-GEOD-21541 | biostudies-arrayexpress
Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.
2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress
Project description:The obligate intracellular human pathogen Chlamydia pneumoniae was subjected to dRNA-Seq to gain insights into the transcriptome. The two distinct life cycle forms elementary bodies (EB) and reticulate bodies (RB) were isolated from human Hep2 cell line by differential gradient centrifugation. Total RNA was isolated and partially treated with Terminator Exonuclease to digest RNA without 5'-PPP and thereby enrich for native 5' ends.
2011-08-18 | E-GEOD-24999 | biostudies-arrayexpress
Project description:Amplification of large chromosomal regions (gene amplification) is a common somatic alteration in human cancer cells and often is associated with advanced disease. A critical event initiating gene amplification is a DNA double strand break (DSB), which is immediately followed by the formation of a large DNA palindrome. Large DNA palindromes are frequent and non-randomly distributed in the genomes of cancer cells and facilitate further increase in copy number. Although the importance of the formation of large DNA palindromes as a very early event in gene amplification is widely recognized, it is not known 1) how a DSB is resolved to form a large DNA palindrome; and 2) whether any local DNA structure determines the location of large DNA palindromes. We show here that intra-strand annealing following a DNA double-strand break leads to the formation of large DNA palindromes and that DNA inverted repeats in the genome determines the efficiency of this event. Furthermore, in human Colo320DM cancer cells, a DNA inverted repeat in the genome marks the border between amplified and non-amplified DNA. Therefore, an early step of gene amplification is a regulated process that is facilitated by DNA inverted repeats in the genome. Experiment Overall Design: Genomic DNA samples from HFF2 and Colo320DM cells were collected and taken through the GAPF procedure. Their GAPF profiles were analyzed using Affymetrix HGU 133A arrays, and the differentially hybridized genes were determined to be significant according to a FDR<0.05
2008-06-14 | E-GEOD-6274 | biostudies-arrayexpress
Project description:To investigate enhancer activity in OE19 cells, we performed CUT&Tag_STARR-seq using antibodies against H3K27ac, BRD4 and MED1 .
2024-09-25 | E-MTAB-14155 | biostudies-arrayexpress
Project description:To investigate enhancer activity in OE19 cells, we performed ATAC_STARR-seq and CUT&Tag_STARR-seq using antibodies against H3K27ac, BRD4 and MED1 .
2024-09-24 | E-MTAB-14083 | biostudies-arrayexpress
Project description:Transcription factors (TFs) in concert with chromatin pathways stably reset transcriptional programs during differentiation. Yet we know little how local sites of chromatin reprogramming are specified and how the estimated 3000 TF encoded in mammalian genomes contribute to chromatin dynamics. To identify candidate TFs we developed an integrated computational approach (Epi-MARA) that models chromatin dynamics in terms of predicted transcription factor binding sites and show that it correctly predicts key TFs involved in epigenome reorganization. When applied to a time course of genome-wide H3 lysine 27 trimethylation (H3K27me3), a chromatin mark set by the Polycomb system, during neuronal differentiation of murine stem cells Epi-MARA predicted that the repressive transcription factor REST contributes to a gain of H3K27me3 at a subset of promoters during the transition from the stem to the progenitor state. To test this prediction we identified, genome-wide, the actual binding sites of REST and H3K27me3 during the differentiation in cells that are either wildtype or in which REST had been deleted. REST indeed localizes to a subset of sites that gain H3K27me3 in progenitors. Importantly, absence of REST in trans leads to a loss of H3K27me3 predominantly in the neuronal progenitor state and specifically at those regions where REST was bound. This function further requires REST binding sites in cis as their mutation leads to substantial loss of H3K27me3. Taken together we provide a novel approach to identify epigenome and TF crosstalk during cellular reprogramming and prove experimentally the prediction that REST acts as an important recruiter of Polycomb repression during early steps of neurogenesis. Dataset comprises of 15 ChIP-seq samples using chromatin from embryonic stem (ES) and neuronal progentor (NP) of wildtype and RESTko cells, which was immunoprecipitated, using antibodies against REST, H3K27me3, or Suz12
2012-09-04 | E-GEOD-27148 | biostudies-arrayexpress
Project description:Histone modification H3K9me2 is associated heterochromatin and gene silencing, but the relationship between DNA methylation and H9K9me2 haven’t been checked in a genome-wide scale. This dataset was generated to compare with genome-wide DNA methylation data. Genome-wide distribution of H3K9me2 in human fibroblasts was mapped using ChIP-chip.
2011-08-28 | E-GEOD-29381 | biostudies-arrayexpress
Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5. Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day. Seedlings were then collected during periods of hypocotyl elongation and stasis for three days. There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates. In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study. Each sample consists of multiple pooled seedlings.
2011-03-31 | E-GEOD-21684 | biostudies-arrayexpress