KAS-seq of Barrett's oesophagus & OAC patients
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Yaoyong Li
PROVIDER: E-MTAB-14091 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:KAS-seq of Barrett's oesophagus & OAC patients
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Project description:To identify eRNA transcripts in OE19 cells, we performed KAS-seq.
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Project description:To investigate changes to eRNA transcripts in the presence and the absence of lapatinib in OE19 cells, we performed KAS-seq on OE19 cells treat with 500 nM lapatinib for 1 day.
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Project description:The open chromatin of Barrett's oesophagus cell line CP-A has been profiled by ATAC-seq.
2020-09-30 | E-MTAB-8994 | biostudies-arrayexpress
Project description:To investigate gene expression profiles of Barrett's oesophagus and oesophageal adenocarcinoma samples, we carried out RNA-seq to identify differentially expressed genes in each disease state.
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Project description:ATAC-seq of human Barrett's oesophagus tissue
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Project description:mucosal biopsies were taken from patients at pre and post-argon plasma coagulation (APC) ablation of Barrett's oesophagus, and from healthy controls. Total RNA was extracted using Trizol. miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel (Life technologies, #4461104). The panel consisted of probes for 754 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v14. Endoscopic surveillance remains the mainstay of cancer prevention in individuals with Barrett’s oesophagus, and definitive management by surgery or endoscopy is reserved for high grade dysplasia or cancer. There are several endoscopic treatments that are widely used for Barrett’s oesophagus, including argon plasma coagulation (APC). The normality of the regenerated neosquamous epithelium after ablation has been called into question. In the current study we profiled global microRNA expression in oesophageal mucosa before and after ablation of Barrett’s oesophagus using Argon plasma coagulation. Our aim was to investigate differences in microRNA expression between neosquamous and normal squamous tissues.
2017-09-14 | GSE94854 | GEO
Project description:ATAC-seq of CP-A Barrett's oesophagus cells
| PRJEB37997 | ENA
Project description:The major aetiological risk factor for Barrett's oesophagus and oesophageal adenocarcinoma is gastroesophageal reflux. This study's aim was to identify genes involved in the celular response to reflux in vitro. The Barrett’s oesophagus cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture. RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays. In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5; 152 genes were up-regulated at 2 hours (91 at 6 hours) and 10 down-regulated at 2 hours (34 at 6 hours). 12 genes were identified and were subsequently assessed in patients with non-erosive reflux disease, oesophagitis, Barrett's oesophagus and oesophageal adenocarcinoma Background and Aims: The major etiological risk factor for Barrett’s esophagus and esophageal adenocarcinoma is gastro-esophageal reflux. This study’s aim was to identify genes involved in the cellular response to components of reflux both in vitro and in patients with reflux-related disease. Methods: The Barrett’s cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture. RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays. 12 genes of interest were analysed by Real Time PCR both in cell line and biopsies from 110 patients with non-erosive reflux disease, esophagitis, Barrett’s esophagus and esophageal adenocarcinoma. Results: In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5. Of 12 genes analysed in biopsies, 10 were significantly different between the 4 groups with the largest change for anterior gradient homolog 2, which may modulate p53 function. This had highest expression in biopsies from Barrett’s esophagus (median gene fold change for Barrett’s esophagus versus non-erosive reflux disease, 411.2 (95% CI 290.5-682.7; p<0.01); esophageal adenocarcinoma versus non-erosive reflux disease 68.1 (20.5-161.4; p<0.01)). In addition 4 genes associated with development/differentiation were upregulated in Barrett’s biopsies compared to those from non-erosive reflux disease (SEL1L, MFNG, CRIP1 and EFNA1). Conclusions: Novel genes have been identified, whose expression is altered after acid and bile exposure in vitro and in biopsies from patients with reflux related diseases. These genes may have utility as biomarkers of response to reflux and should be assessed in prospective studies. Keywords: Acid (pH 4.5) and bile (mixture of primary bile salts or the secondary bile salt deoxycholic acid, both at pH 4.5) challenge to a Barrett's oesophagus cell line. RNA extraction at 2 and 6 hours. Comparison of treatment RNA to control (non-treatment) RNA,
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