Similar Datasets
Project description:To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma miRNAs expression in human cholangiocarcinoma/normal bile duct samples was measured after operation.Three independent experiments were performed using different patients for each experiment.
2013-06-10 | E-GEOD-47764 | biostudies-arrayexpress
Project description:Transcriptional profiling of Lactobacillus reuteri ATCC 55730 mid-log cultures before vs after exposure to 0.5% bovine bile (oxgall). Two sets of array experiments were performed. One set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had been exposed to 0.5% bile for 15 minutes (bile shock). The other set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had begun growing again in the presence of 0.5% bile (bile adaptation). Keywords: Stress response
2008-02-05 | GSE10155 | GEO
Project description:Unlike many other types of diarrheagenic bacteria that act primarily in the small intestine, O157:H7 expresses virulence primarily in the large intestine. In this study, microarray analysis is employed to examine the transcriptional response of O157:H7 to bile treatment, to gain insight into how bile affects virulence and whether bile might be temporally defending the small intestine against virulence by these bacteria. Keywords: Expression profiling of two different growth conditions
2012-07-31 | GSE20380 | GEO
Project description:To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma
2013-06-10 | GSE47764 | GEO
Project description:Unlike many other types of diarrheagenic bacteria that act primarily in the small intestine, O157:H7 expresses virulence primarily in the large intestine. In this study, microarray analysis is employed to examine the transcriptional response of O157:H7 to bile treatment, to gain insight into how bile affects virulence and whether bile might be temporally defending the small intestine against virulence by these bacteria. Keywords: Expression profiling of two different growth conditions Two groups of three replicates were used: E.coli O157:H7 grown in Luria broth with or without 0.8% bile salts
2012-07-30 | E-GEOD-20380 | biostudies-arrayexpress
Project description:Transcriptional profiling of Lactobacillus reuteri ATCC 55730 mid-log cultures before vs after exposure to 0.5% bovine bile (oxgall). Two sets of array experiments were performed. One set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had been exposed to 0.5% bile for 15 minutes (bile shock). The other set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had begun growing again in the presence of 0.5% bile (bile adaptation). Two sets of two condition experiments: Set one: before bile treatment and 15 minutes after bile treatment. Biological replicates: 5 untreated and 5 treated, independently grown and collected. Two replicates per biological replicate (dye-swap). Set two: before bile treatment and after the resumption of growth in the presence of bile. Biological replicates: 5 untreated and 5 treated, independently grown and collected. Two replicates per biological replicate (dye-swap).
2010-05-26 | E-GEOD-10155 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and tumor bile duct samples. The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 138 tumor bile duct samples and 4 normal bile duct samples.
2017-07-03 | GSE89803 | GEO
Project description:Assays in bile duct cancer patients showed 984 CNVs in 306 CNV regions (CNVR) distributed throughout all 22 chromosomes. Bile duct cancer patients had a mean of 21.8 gains and 19.2 losses of genes, with an average of 35.9 CNVRs per patient. Frequent sites of gains were at chromosomes 22q11.22, 2p11.2-p.11.1, 14q32.33 and 17q12, whereas frequent sites of losses were at 19q12-q13.43. Investigation of CNV in 24 bile duct cancer tissue samples
2013-07-13 | E-GEOD-48835 | biostudies-arrayexpress
Project description:Purpose: To analyze human and bacteria proteomic profiles in bile, exposed to a tumor vs. non-tumor microenvironment, in order to identify differences between these conditions, which may contribute to a better understanding of pancreatic carcinogenesis. Patients and Methods: Using liquid chromatography and mass spectrometry, human and bacteria proteomic profiles of a total of 20 bile samples (7 from gallstone (GS) patients, and 13 from pancreatic head ductal adenocarcinoma (PDAC) patients) that were collected during surgery, and taken directly from the gallbladder were compared. g:Profiler and KEGG (Kyoto Encyclopedia of Genes and Genomes) Mapper Reconstruct Pathway was used as the main comparative platform focusing on over-represented biological pathways among human proteins and interaction pathways among bacterial proteins. Results: Three bacterial infection pathways were over-represented in the human PDAC group of proteins. IL-8 is the only human protein that coincides in the three pathways and this protein is only present in the PDAC group. Quantitative and qualitative differences in bacterial proteins suggest a dysbiotic microenvironment in the PDAC group, supported by significant participation of antibiotic biosynthesis enzymes. Prokaryote interaction signaling pathways highlight the presence of zeatin in the GS group and surfactin in the PDAC group, the former in the metabolism of terpenoids and polyketides, and the latter in both metabolisms of terpenoids, polyketides and quorum sensing. Based on our findings, we propose a bacterial-induced carcinogenesis model for the biliary tract. Conclusion: To the best of our knowledge this is the first study with the aim of comparing human and bacteria bile proteins in a tumor vs. non-tumor microenvironment. We proposed a new carcinogenesis model for the biliary tract based on bile metaproteomic findings. Our results suggest that bacteria may be key players in biliary tract carcinogenesis, in a long-lasting dysbiotic and epithelially harmful microenvironment, in which specific bacterial species biofilm formation is of utmost importance. Our finding should be further explored in future using in vitro and in vivo investigations
2020-07-08 | PXD020151 | Pride
Project description:Bbr_0838 from Bifidobacterium breve UCC2003 encodes a 683 residue membrane protein, that contains a permease domain displaying similarity to transporters belonging to the major facilitator superfamily, as well as a CBS (cystathionine beta synthase) domain. The high level of similarity to bile-efflux pumps from other bifidobacteria, suggests a significant role for Bbr_0838 in bile tolerance of B. breve UCC2003. Bbr_0838 transcription was shown to be monocistronic and strongly induced upon exposure to bile. Further analysis delineated the transcriptional start site and the minimal region required for promoter activity and bile regulation. Insertional inactivation of Bbr_0838 in B. breve UCC2003 resulted in a strain that exhibited reduced survival upon cholate exposure as compared to the parent strain, a phenotype that was reversed when a functional Bbr_0838 gene was introduced into UCC2003::838800. Transcriptome analysis of UCC2003::838800 grown in the presence or absence of bile demonstrated that transcription of Bbr_0832, which is predicted to encode a macrolide-efflux transporter gene, was significantly increased in the presence of bile, representing a likely compensatory mechanism for bile removal in the absence of Bbr_0838. This study represents the first in depth analysis of a bile-inducible locus in bifidobacteria, identifying a key gene relevant for bifidobacterial bile tolerance. In order to investigate differences in global gene expression upon growth or exposure of B. breve UCC2003-delta0838 to cholic acid compared to normal growing cells, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003-delta0838 cultures under normal conditions and cultures grown on or exposed to cholic acid. All experiments were performed in duplo and targets where confirmed with QRT-PCR. In addition transcriptome analyse was performed of B. breve UCC2003 compared to that of B. breve UCC2003-delta0838 both exposed to 0.1 % cholic acid. This was performed as a single experiment and targets were confirmed by QRT-PCR
2012-02-20 | E-GEOD-31224 | biostudies-arrayexpress