HIF2A(EPAS1) Genome-Wide Localization in MRC5 Human Fibroblasts by Cut & Tag
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB72033 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12525247_1.fastq.gz | Fastqsanger.gz | |||
| ERR12525247_2.fastq.gz | Fastqsanger.gz | |||
| ERR12525248_1.fastq.gz | Fastqsanger.gz | |||
| ERR12525248_2.fastq.gz | Fastqsanger.gz | |||
| ERR12525249_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:HIF2A(EPAS1) geenome_wide localization by Cut & Tag in MRC5 human fibroblasts ectopically expressing HIF2A in the pBabe vector, and in control MRC5 human fibroblasts containing only the pBabe vector. 2 biological replicates were done for the MRC5-HIF2A cells. Cut & Tag with an anti-H3-K27me3 Ab was done as a positive control for the Cut & Tag experiments.
2025-01-17 | E-MTAB-13732 | biostudies-arrayexpress
Project description:Expression profiling of MRC5, IFN gamma treated MRC5 and PGF cells. Keywords: cell type comparison, IFN gamma treatment.
2008-07-01 | GSE10880 | GEO
Project description:Purpose: By integrating DNA methylation and gene expression of COPD lung tissues, we identified EPAS1 as a key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms of methylation profiles and downstream target genes. Genes predicted to be regulated by EPAS1 were enriched for biological processes including signaling, cell communications, and system developement. As EPAS1 downstream genes were significantly enriched for hypoxia responsive genes in endothelial cells, we tested EPAS1 function in human and mouse endothelial cells HUVEC and C166. EPAS1 knockdown by siRNA in endothelial cells impacted genes that significantly overlapped with EPAS1 downstream genes in lung tissue including hypoxia responsive genes. Methods: The cell lines of HUVEC (Lonza, MD, USA) and C166 (American Type Culture Collection, VA, USA) were cultured in the appropriate media at 37M-BM-0C with 5% CO2. The cells were transfected with EPAS1 siRNA and non-targeting negative control siRNA (Life Technologies, CA, USA) using Lipofectamine RNAiMAX as recommended transfection protocols by the manufacturer. After the treatments with 5nM SilencerM-BM-. Select siRNA (s4700 for EPAS1, s65525 for Epas1; Life Technologies, USA) for 48 hours, the total RNA was purified with RNeasy Mini Kit (QIAGEN, Germany). The efficiencies of knocked down the EPAS1 expression were assessed by qPCR with 1.4% for HUVEC, 3.2% for C166. Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions. Sequence reads were aligned to human genome assembly hg19 and mouse genome assembly mm10, respectively, using Tophat [96]. Total 23,228 human and 22,609 mouse genes were quantified using Cufflinks [96]. siRNA signatures were derived by comparing expression profiles of EPAS1 or Epas1 siRNAs with non-targeting siRNAs at paired t-test p-value cutoff 0.05 with resulting signature sizes of 2,796 and 3,730, and corresponding q-values [97] 0.11 and 0.07 for HUVEC and C166, respectively. Results: When comparing endothelial cells treated with EPAS1 siRNAs and scrambled siRNAs, we identified an EPAS1 siRNA signature consisting of 2796 and 3730 genes in human and mouse endothelial cell lines, respectively, whose expression levels significantly changed (t-test p-value<0.05), including EPAS1 itself (p-value = 0.002 and 0.02) and the EPAS1 downstream target gene VEGFA (p-value = 0.03 and 0.01). The EPAS1 siRNA signatures derived from human and mouse cell lines were highly consistent, with 695 genes in common to both signatures (p-value = 7.2x10-65). Both signatures not only significantly overlapped with EPAS1 downstream genes (p-value = 7.3x10-7 and 1.5x10-12), but also with hypoxia response genes in endothelial cells (FisherM-bM-^@M-^Ys Exact Test p-value = 5.8x10-8 and 1.2x10-12 in the human and mouse signatures, respectively). Moreover, the EPAS1 siRNA signatures consistently overlapped genes associated with the COPD severity phenotypes. These results together validate that EPAS1 causally regulates the downstream target genes we predicted, and that these genes in turn affect COPD development and progression. For each of human and mouse cell lines, 3 siRNA control cells, and 3 siRNA EPAS1 knockdown cells were used and analyzed. To identify EPAS1 signatures, paired t-test was performed between control siRNA and EPAS1 siRNA samples.
2015-01-16 | E-GEOD-62974 | biostudies-arrayexpress
Project description:HIF2a function is both necessary and sufficient for the growth of VHL-null clear cell Renal Cell Carcinoma (ccRCC). Targeting HIF2a function can therefore be a promising therapeutic strategy. We used microarray analysis to characterize a novel pharmacological inhibitor of HIF2a named PT2399. By comparing genes that are responsive to PT2399 in parental cells vs cells lacking HIF2a, by virtue of CRISPR-mediated genetic editing, we characterized gene signatures that are regulated by PT2399 in a HIF2a dependent manner. Cells were treated with either DMSO (control) or 2uM PT2399 for indicated time periods, total RNA was extracted and analyzed. Please note that the experiments with 786O Parental and HIF2a null cells were conducted independently.
2016-07-03 | E-GEOD-72959 | biostudies-arrayexpress
Project description:Expression profiling of MRC5, IFN gamma treated MRC5 and PGF cells. Experiment Overall Design: MRC5 cells were treated for 24 hours with IFN gamma (200 IU/ml) and their expression profile was compared to untreated MRC5 and PGF cells.
2008-10-20 | E-GEOD-10880 | biostudies-arrayexpress
Project description:To understand the role of the hypoxia-inducible transcription factor EPAS1 in regulating spermatogonial stem cell (SSC) function, a conditional knockout mouse was generated (EPAS1-cKO) where Epas1 was ablated only in the germ cells (Ddx4-Cre, Epasfl/-). For single cell RNA sequencing analysis, control and EPAS1-cKO males were pre-treated with the chemotherapeutic reagent busulfan to instigate regenerative conditions, and a germ cell-enriched cell population was collected 14 days later. Transcriptome profiling revealed that EPAS1 deficiency alters gene expression and key cellular processes in undifferentiated spermatogonia, including metabolism and proteostasis. Overall, these transcriptomic changes resulted in an impaired capacity for SSCs to restore spermatogenesis after busulfan treatment.
2023-11-08 | GSE235319 | GEO
Project description:Purpose: to investigate the human transcriptome in MRC5 fibroblasts
2022-12-18 | GSE171519 | GEO
Project description:H3K27me3 localization in UTX deficient Plasma cells by CUT&Tag
| PRJNA767652 | ENA
Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. We generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells). In analysis of AT-iPS cells, the human wild-type iPS cell line (MRC5-iPS) was generated and cultured in the same conditions as the diseased iPS cell lines. It is an ideal control cell line for the disease and patient-specific iPS cell lines. Because MRC5-iPS cells exhibited considerable chromosomal abnormalities in vitro, we performed a structural alteration analysis by using a SNP genotyping array for MRC5-iPS cell line, Tic, at passage 15, passage 30, and passage 37.
2013-07-23 | GSE49082 | GEO
Project description:HIF2a function is both necessary and sufficient for the growth of VHL-null clear cell Renal Cell Carcinoma (ccRCC). Targeting HIF2a function can therefore be a promising therapeutic strategy. We used microarray analysis to characterize a novel pharmacological inhibitor of HIF2a named PT2399. By comparing genes that are responsive to PT2399 in parental cells vs cells lacking HIF2a, by virtue of CRISPR-mediated genetic editing, we characterized gene signatures that are regulated by PT2399 in a HIF2a dependent manner.
2016-01-01 | GSE72959 | GEO