Browse
Submit Data
Databases
API
Help

Dataset Information

61 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human hepatic arteries in a study of primary sclerosing cholangitis

ABSTRACT: PSC is a chronic inflammatory condition of the biliary tree causing biliary strictures and fibrosis and predisposes to cholangiocarcinoma. Traditionally it is considered a primary disorder of the bile duct epithelia. Here we investigate whether injury to the arterial blood supply may contribute to PSC. Hepatic arteries were collected from 8 patients at the time of liver transplantation: 4 with PSC and 4 disease controls. Samples were used for RNA-sequencing, differential expression and pathways analyses.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Perla Troncoso-Rey

PROVIDER: E-MTAB-11917 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Serum and bile proteomics reveal candidates for new noninvasive serum markers of primary sclerosing cholangitis and of risk of disease progression and biliary neoplasia.

Project description:Primary sclerosing cholangitis (PSC) is a chronic liver disease characterized by biliary strictures, cholestasis, and an increased risk of cholangiocarcinoma (CCA). Here, we have used label-free quantitative proteomics to analyze serum and bile samples from non-PSC controls and PSC patients, as well as from PSC patients divided into groups according to endoscopic retrograde cholangiography score (with a score of >4 indicating advanced disease) and presence or absence of biliary dysplasia/CCA. Further analyses subsequently identified multiple candidates of new noninvasive serum markers for the diagnosis of PSC, as well as new markers for the prediction of the risk of disease progression and biliary neoplasia for patients already diagnosed with PSC.

2022-08-03 | PXD026693 | Pride

Serum and bile proteomics reveal candidates for new noninvasive serum markers of primary sclerosing cholangitis and of risk of disease progression and biliary neoplasia (BILE)

2022-08-03 | PXD026694 | Pride

Purified intestinal epithelial cells from foetal and paediatric gut

Project description:CD326+ sorted intestinal epithelial cells from foetal (9-12 wk gestational age) small bowel and large bowel, CD326+ sorted intestinal epithelial cells from mucosal biopsies of paediatric (5-15 years of age) terminal illeum, ascending colon and sigmoid colon FPG=Foetal proximal gut, FDG=Foetal distal gut, PTI=paediatric terminal ileum, PAC=paedaitric ascending colon, PSC=paediatric sigmoid colon

2015-09-15 | E-MTAB-3704 | biostudies-arrayexpress

Purified intestinal epithelial cells from foetal and paediatric gut

2015-09-15 | E-MTAB-3703 | biostudies-arrayexpress

The role of Clec4e (Mincle) in microglia response to transient ischemic injury

Project description:This data set shows dramatic changes in gene expression in microglia isolated from C57Bl6/J mice subjected to transient middle cerebral artery occlusion, as compared to those subjected to sham surgery. Mice deficient in Mincle (Clec4e-/-) showed significantly improved injury outcomes 3 and 7 days after transient middle cerebral artery occlusion. However, when comparing changes in gene expression in microglia 24 hours after blood reperfusion, there were no differences between wild-type and Clec4e-/- mice, indicating that Mincle does not participate in early microglial activation. Wild type and Mincle knock-out (Clec4e-/-) mice. After 1 h of transient middle cerebral artery occlusion (tMCAO) and 24 h of reperfusion, mice were perfused with PBS, their brains dissected, and 2 ipsilesional hemispheres (with cerebellum and brainstem removed) pooled for microglia isolation. For sham-operated animals, the whole forebrain was used and brains were not pooled. After myelin separation by Percoll gradient centrifugation, around 80,000 CD45intermediate, CD11b+ microglial cells were sorted from each sample. Sham samples n=3, tMCAO samples n=5.

2016-03-24 | E-GEOD-77986 | biostudies-arrayexpress

Is Increased Sinusoidal Flow in the Liver Remnant the primary Stimulus to Regeneration after partial Hepatectomy

Project description:The impact of portal arterialization on the liver parenchyma was studied in a series of six pigs with aortoportal shunting of liver segments II, III and IV (and 6 sham animals). Gene expression in the arterialized segments was compared to expression in sham animals. Primary endpoints were gene expression profiles in the hyperperfused segments at sampling time points 1, 5, 10, 30, 60, 90 minutes and 2, 3, 4 and 6 hours after shunt opening. Keywords: time course, treatment comparison Six pigs were treated with aortoportal shunting of segments II, III and IV and six animals were subject to sham surgery. Expression profiling was conducted by hybridizing each sample against a common reference, consisting of liver RNA from an unrelated animal..

2010-05-07 | E-GEOD-13683 | biostudies-arrayexpress

Downregulation of TGR5 (GPBAR1) in biliary epithelial cells is characteristic of sclerosing cholangitis and may contribute to disease pathogenesis

Project description:Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation and progressive fibrosis of the biliary tree. The bile acid receptor TGR5 is found on biliary epithelial cells (BECs), where it promotes secretion, proliferation and tight junction integrity. Thus, we speculated that changes in TGR5 expression in BECs may contribute to PSC pathogenesis.

2021-03-12 | GSE168758 | GEO

Proteome and phosphoproteome of hippocampus after focal cerebral ischemia 2 h in mice

Project description:We obtained the profiles of neuronal phosphoproteome after cerebral ischemia onset by isolating mice hippocampus. Hippocampus combined from either ten sham or ten focal cerebral ischemia 2 h mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. Five percent of the pool was used for whole proteome analysis, and the remaining 95% was subjected to phosphoproteome profiling. In total, we quantified 5,174 proteins and 9,062 phosphopeptides. Interesting, 21 proteins were upregulated and 7 proteins were downregulated in hippocampus lysates of cerebral ischemia 2 h relative to sham base on fold change. S100a9, Alpha-2-HS-glycoprotein (Ahsg), Fibrinogen beta chain (Fga) and Complement Component C3(c3) are the top significantly changed, which were highly consistent with previous reports in cerebral ischemia injury. Using wolfpsort software to analysis the Subcellular Location, 57% of detected proteins were location to extracellular, 15% were cytoplasmic protein, another 11% were transport to nucleus, and the others were location to plasma membranes (10%), mitochondria (4%) and endoplasmic reticulum (3%). Moreover,184 phosphorylation sites of 135 proteins were upregulated and 689 phosphorylation sites of 420 proteins were downregulated in hippocampus during cerebral ischemia 2 h compare with sham operation. Employing wolfpsort software analysis the subcellular location, 50% of phosphorylated proteins were location to nucleus, 26% were cytoplasmic protein, another 16% were transport to plasma membranes, and the others were location to mitochondria (4%), extracellular (3%) and cytoskeleton (1%). Motif analysis showed that 85% were belongs to serine-type phosphorylation, about 14 were threonine-type phosphorylation and 1% were tyrosine-type phosphorylation.

2022-03-14 | PXD027145 | Pride

phosphoproteome of hippocampus after focal cerebral ischemia 1.5 h and reperfusion 24 h in mice

Project description:We obtained the profiles of neuronal phosphoproteome after cerebral ischemia and reperfusion by isolating mice hippocampus. Hippocampus combined from either nine sham or nine focal cerebral ischemia 1.5 h and reperfusion 24 h (IR) mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. In total, we quantified 7,865 phosphopeptides,179 phosphorylation sites of 129 proteins were upregulated and 843 phosphorylation sites of 494 proteins were downregulated in hippocampus during cerebral ischemia 2 h compare with sham operation.

2024-02-15 | PXD033851 | Pride

Proteome of hippocampus after focal cerebral ischemia 1.5 h and reperfusion 24 h in mice

Project description:We obtained the profiles of neuronal proteome after cerebral ischemia and reperfusion by isolating mice hippocampus. Hippocampus combined from either nine sham or nine focal cerebral ischemia 1.5 h and reperfusion 24 h (IR) mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. In total, we quantified 5,059 proteins. We identified 142 differentially expressed proteins (t-test, p-value<0.05) after IR compared to sham groups. The results showed that 92 proteins were upregulated, and 50 proteins were downregulated after IR compared to sham groups. Gene ontology (GO) enrichment analysis of differentially expressed proteins between sham and IR groups. The results showed that the biological process of most of upregulated genes linked with immune inflammatory related responses were increased. And KEGG pathway analysis for upregulated genes showed that multiple immune inflammatory response pathways also increased significantly, such as TNF-signaling, NF-κB signaling and cytokine-cytokine receptor interaction, as well as NOD-like receptor signaling, and toll-like receptor signaling.

2024-02-15 | PXD033938 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data