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TranscriptomicsTranscriptional profiling after bile duct ligation identifies PAI-1 as a contributor to cholestatic injury in mice.
Extrahepatic cholestasis leads to complex injury and repair processes that result in bile infarct formation, neutrophil infiltration, cholangiocyte and hepatocyte proliferation, extracellular matrix remodeling, and fibrosis. To identify early molecular mechanisms of injury and repair after bile duct...
ORGANISM(S): Mus musculus 
2011-06-09 | E-GEOD-29776 | biostudies-arrayexpress
GenomicsMassive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma
Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Methods: mRNA and...
ORGANISM(S): Homo sapiens 
2015-01-22 | E-GEOD-63420 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA sequencing of the human biliary tree
scRNA-seq of intrahepatic and extrahepatic (common bile duct and gallbladder) adult primary human cholangiocytes
ORGANISM(S): Homo sapiens 
2021-03-12 | E-MTAB-8495 | biostudies-arrayexpress
TranscriptomicsA novel 3-D organotypic culture model by co-culturing alpha-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix
The increased M-NM-1-smooth muscle-actin positive cancer-associated fibroblastic cells (CAF) in the desmoplastic stroma may relate to a more aggressive cancer and worse survival outcomes for intrahepatic cholangiocarcinoma (ICC) patients We developed a novel 3-D organotypic culture model by co-cultu...
ORGANISM(S): Rattus norvegicus 
2012-06-22 | E-GEOD-38889 | biostudies-arrayexpress
TranscriptomicsGene-expression profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients. METHODS: We performed gene expression profile, high-density single nucleot...
ORGANISM(S): Homo sapiens 
2013-01-24 | E-GEOD-32225 | biostudies-arrayexpress
TranscriptomicsDNA copy number profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients. METHODS: We performed gene expression profile, high-density single nucleot...
ORGANISM(S): Homo sapiens 
2013-01-24 | E-GEOD-33326 | biostudies-arrayexpress
TranscriptomicsRegional differences in human biliary tissues and corresponding in vitro derived organoids
RNA-Sequencing was performed on mechanically dissociated, epithelial-enriched samples, of human extrahepatic biliary tissue from Gallbladder, Common Bile Duct, and Pancreatic Duct tissues. Sequencing was also performed on in vitro cultures of Organoid cell lines at passage 5 that were derived from h...
ORGANISM(S): Homo sapiens 
2019-01-20 | E-MTAB-7569 | biostudies-arrayexpress
TranscriptomicsIntegrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients. METHODS: We performed gene expression profile, high-density single nucleot...
ORGANISM(S): Homo sapiens 
2013-01-24 | E-GEOD-33327 | biostudies-arrayexpress
TranscriptomicsIntegrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma
This SuperSeries is composed of the following subset Series: GSE32879: Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma [mRNA] GSE32957: Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenoty...
ORGANISM(S): Homo sapiens 
2012-09-28 | E-GEOD-32958 | biostudies-arrayexpress
TranscriptomicsComprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls
Liver biopsy samples were obtained from 64 infants with biliary atresia at the time of intraoperative cholangiogram. Liver biopsy samples were obtained from 14 age-matched infants with other causes of intrahepatic cholestasis, and from 7 deceased-donor children. GeneChip® Human Gene 1.0 ST Array (Af...
ORGANISM(S): Homo sapiens 
2013-06-01 | E-GEOD-46960 | biostudies-arrayexpress
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