ATAC-sequencing in control and Stag2 knockdown cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Jasper Mullenders
PROVIDER: E-GEOD-72367 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We performed ATAC-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for either Renilla or Stag2.
2015-09-16 | GSE72367 | GEO
Project description:We performed RNA-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for Renilla, Smc1a or Stag2. RNA-sequencing control (Renilla) and cohesin (Smc1a and Stag2) knockdown cells.
2015-09-16 | E-GEOD-72369 | biostudies-arrayexpress
Project description:We performed RNA-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for Renilla, Smc1a or Stag2.
2015-09-16 | GSE72369 | GEO
Project description:We performed RNA-sequencing in c-Kit+ cells that were infected with retroviruses expressing shRNAs for Renilla, Rad21, Smc1a, Smc3 or Stag2. These cells were grown in methylcellulose (M3434) for either one passage (P1) or replated for five passages (P5). RNA-sequencing control (Ren) and cohesin (Rad21, Smc1a, Smc3 and Stag2) knockdown cells.
2015-09-16 | E-GEOD-72368 | biostudies-arrayexpress
Project description:STAG2 is targeted by somatic aberrations in a subset (4%) of human PDAs. Transposon mediated disruption of STAG2 in a KRASG12D genetically engineered mouse model promotes the development of PDA and its progression to metastatic disease. There was a statistically significant loss of STAG2 protein expression in human tumor tissue (Wilcoxon-Rank test) with complete absence of STAG2 staining observed in 15 (4.3%) patients. In univariate Kaplan Meier analysis nearly complete STAG2 positive staining (> 95% of nuclei positive) was associated with a median survival benefit of 6.41 months (p = 0.031). The survival benefit of adjuvant chemotherapy was only seen in patients with a STAG2 staining of less than 95% (median survival benefit 7.65 months; p = 0.028). Multivariate Cox Regression analysis showed that STAG2 is an independent prognostic factor for survival in pancreatic cancer patients. Finally we show that RNAi mediated knockdown of STAG2 selectively sensitizes human PDA cell lines to platinum-based therapy. We used DNA content flow sorting to identify and purify tumor nuclei of PDA samples from 50 patients. The genome of each sorted sample was profiled by oligonucleotide comparative genomic hybridization (aCGH) and targeted resequencing of STAG2. Transposon insertions within STAG2 in a KRASG12D driven genetically engineered mouse (GEM) model of PDA were screened by RT-PCR. We then used a tissue microarray (TMA) to survey STAG2 protein expression levels in 344 human PDA tumor samples and adjacent tissues. Univariate Kaplan Meier analysis and multivariate Cox Regression analysis was used to assess the association of STAG2 expression relative to overall survival and responses to adjuvant therapy. Finally RNAi based assays with PDA cell lines were used to assess the potential therapeutic consequence of STAG2 expression in responses to 18 therapeutic agents.
2014-01-24 | E-GEOD-54328 | biostudies-arrayexpress
Project description:Expression analysis of OS tumors with shRNA knockdown of PTHR1 mouse OS 80 (a Cre:lox OS cell line from Boston) was tagged with firefly luciferase expression construct. They were then infected with either control (renilla luciferase shRNA) or an shRNA that effective knocks-down PTHR1 (PTHR1.358; para-thyroid hormone receptor). The cells were injected with matrigel onto the back flank of Balb/c nu/nu mice and left to grow for 1 month with weekly monitoring of tumour size by in vivo luciferase assay. At 4 weeks the tumours were removed and trizol stored. Whole tumour was ground up and set form micro-array. 6 tumors with shRNA PTHR1 knockdown ; 6 tumors with shRNA control (renilla luciferase shRNA) knockdown
2015-07-01 | E-GEOD-46861 | biostudies-arrayexpress
Project description:STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy Gene copy number analyses of STAG2 in urinary bladder tumors. R values were extracted from beadstudio and normalised using the pounds method. Log R Ratios were calculated using an average value of R from 200 cases and controls from the Epicuro study. WaviCGH was used to generate copy number calls and log R ratios in the region of STAG2 on the X chromosome were also visualised manually to determine STAG2 loss.
2013-10-24 | E-GEOD-51589 | biostudies-arrayexpress
Project description:STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy Gene copy number analyses of STAG2 in urinary bladder tumors. R values were extracted from beadstudio and normalised using the pounds method. Log R Ratios were calculated using an average value of R from 200 cases and controls from the Epicuro study. WaviCGH was used to generate copy number calls and log R ratios in the region of STAG2 on the X chromosome were also visualised manually to determine STAG2 loss.
2013-10-24 | E-GEOD-51640 | biostudies-arrayexpress
Project description:Aneuploidy is among the most common hallmarks of cancer, yet the underlying genetic mechanisms are still poorly defined. We have recently identified STAG2 as a gene that is mutated in human cancer and whose inactivation leads directly to chromosomal instability and aneuploidy. However, no single tumor type has yet been identified in which inactivation of a cohesin subunit represents a predominant mutational event. Here we used immunohistochemistry to screen a panel of 2,214 tumors from each of the major human tumor types to identify additional tumor types harboring somatic loss of STAG2. Strikingly, STAG2 expression was completely absent in 18% of urothelial carcinomas, the most common type of bladder cancer and the fifth most common cancer in the United States. DNA sequencing revealed that somatic mutations of STAG2 were present in 21% of urothelial carcinomas, which were found to be a group of highly aneuploid tumors. The acquisition of STAG2 mutations was shown to be an early event in the pathogenesis of urothelial carcinoma. STAG2 loss was significantly associated with lymph node invasion, increased disease recurrence, and reduced cancer-specific survival. These results identify STAG2 as one of the most commonly mutated genes in bladder cancer discovered to date, and demonstrate that STAG2 inactivation defines an aggressive subtype of bladder cancer with particularly poor prognosis. Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from snap-frozen human urothelial carcinoma primary tumors. Copy number analysis using Affymetrix CytoScan HD Arrays was performed for 12 human urothelial carcinomas of the bladder with truncating mutations of the STAG2 gene.
2013-06-30 | E-GEOD-41581 | biostudies-arrayexpress
Project description:The Zinc finger protein of the cerebellum 2 (Zic2) is one of the vertebrate homologs of the Drosophila pair-rule gene odd-paired (opa). Our molecular and biochemical studies have demonstrated that Zic2 to preferentially bind to transcriptional enhancers and functions as a cofactor that interacts with the NuRD complex in ES cells. Detailed genome-wide studies demonstrate that Zic2 function with Mbd3/NuRD in regulating the chromatin state and transcriptional output of genes linked to differentiation. Zic2 is dispensable for the selfrenewal of ES cells but is required for proper differentiation, similar to what has been previously reported for Mbd3/NuRD. Our study identifies Zic2 as a key factor in the execution of the pluripotency program with Mbd3/NuRD in ES cells. ChIP-seq of Zic2, Chd4, Mbd3 and Zic3 in mES cells. ChIP-seq of H3K27me3, H3K27ac, H3K4me3, H3K4me1 and PolII in mES cells after Zic2 shRNA and non-targeting shRNA. RNA-seq of mES cells after Zic2, Zic3, Mbd3 and Mta2 shRNA and non-targeting shRNA.
2015-02-23 | E-GEOD-61188 | biostudies-arrayexpress