Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Seq of Alagille liver biopsies

ABSTRACT: Needle biopsies were performed to obtain liver samples from patients for clinical purposes from patients with Alagille syndrome. A small portion was snap frozen and later used for RNA sequencing analysis. Needle biospies from 5 patients with other liver disorders were included as controls.

ORGANISM(S): Homo sapiens

PROVIDER: GSE104873 | GEO | 2017/10/13

SECONDARY ACCESSION(S): PRJNA414076

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA Seq of Alagille liver biopsies

Project description:RNA Seq of Alagille liver biopsies

| PRJNA414076 | ENA

Human colon biopsies (healthy and Ulcerative Colitis) LC-MS/MS

Project description:The etiology of the inflammatory bowel diseases, including ulcerative colitis, remains incomplete, but recent findings points to the involvement of complex host-microbial interactions. We hypothesized that an analysis of the proteins on the host-microbial interacting surface, the intestinal mucosa, could reveal novel insights into the diseases. Mucosal colonic biopsies were extracted by standard colonscopy from sigmoideum from 10 ulcerative colitis patients from non-inflammed tissue and 10 controls. The biopsies were immediately following extraction snap-frozen for protein analysis and the protein content of the biopsies was characterized by high-throughput quantative gel-free proteomics.

2015-05-26 | PXD001608 | Pride

(Phospho)proteomics profiling of pre-treatment HER2+ BC biopsies

Project description:In this study, we perform (phospho)proteomics analysis of 45 pre-treatment HER2+ needle biopsies of early-stage invasive breast cancer to identify molecular signatures predictive of treatment response to Trastuzumab, Pertuzumab and chemotherapy. All patient biopsies included in this study were classified as HER2+ with a minimum tumour grade of two and tumour cell density of 60% or higher. After needle biopsies were taken, patients completed multiple drug treatment cycles according to the regime of the TRAIN2 study. Finally, treatment response was determined at surgery. The systemic treatment response was categorised as pathological complete response (pCR = ypT0/isypN0) (n=26), near pCR (npCR) (n=8), or No pCR (n=11).

2023-09-20 | PXD034643 | Pride

Human colon biopsies (healthy and Ulcerative Colitis) LC-MS/MS

2017-03-31 | MSV000080833 | MassIVE

Phosphoproteomics scaled-down to tumor biopsy level. Part 2: biopsies

Project description:Mass spectrometry-based phosphoproteomics of tumor tissue or cell line lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of the individual patient’s tumor biology, analysis of the phosphoproteome should be feasible and reproducible using tumor needle biopsies. We hereto scaled down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and show its performance using colorectal cancer (CRC) cell line and needle biopsies from patients. In this study, the feasibility of label-free pTyr-phosphoproteomics at the biopsy level is demonstrated. Unsupervised cluster analysis shows that this approach can identify patient-specific profiles, which will improve our understanding of individual tumor biology and may enable future pTyr-phosphoproteomics-based TKI treatment selection.

2019-10-28 | PXD003814 | Pride

The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers

Project description:Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account. Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes

2008-09-09 | GSE12072 | GEO

Transcription profiling of human biopsies of Nasopharyngeal carcinoma (NPC) and non-malignant controls

Project description:Nasopharyngeal carcinoma (NPC) is a common cancer in southern China and South East Asia where more than 50,000 new cases are diagnosed each year. We used microarrays to identify down or upregulated genes in NPC compared with non-malignant controls. Experiment Overall Design: Snap frozen nasopharyngeal biopsies from 25 patients with histologically confirmed undifferentiated NPC were included in the microarray analysis. Controls were obtained from 3 patients with no evidence of malignancy.

2009-11-10 | E-GEOD-13597 | biostudies-arrayexpress

An optimized protocol for isolation of hepatic leukocytes retrieved from murine and NASH liver biopsies

Project description:Immune dysregulation and inflammation by hepatic-resident leukocytes is considered a key step in disease progression of Non-alcoholic fatty liver disease (NAFLD) and Nonalcoholic steatohepatitis (NASH) toward cirrhosis and hepatocellular carcinoma (HCC). Here we provide a robust protocol for isolation and characterization of liver-resident immune cells from fine needle biopsies of rodent model and human. Various downstream applications can then be applied to gain an appreciation of the functional activity of liver-resident leukocyte populations.

2023-10-03 | GSE230131 | GEO

Microarray gene expression analysis of pinch biopsies from terminal ileum of patients with active and inactive Crohn’s disease and healthy controls

Project description:Biopsies from six individuals of each of the categories active CD (CDA), inactive CD (CD) and healthy controls (N) were analyzed for gene expression using microarray. The biopsies were obtained by ileo-colonoscopy and snap-frozen in nitrogen before RNA-isolation. A gastrointestinal pathologist classified the biopsies into normal, chronic active or chronic inactive inflammation based on Hematoxylin-Eosin stain of tissue sections from adjacent biopsies. Samples with discrepancy between endoscopic and histologic diagnoses were excluded from the final analysis, and uploaded with "NaN". The patients with chronic inactive inflammation all previously had verified CD of the terminal ileum. Patients coming to endoscopy for other reasons than IBD and with normal endoscopic and histological findings served as controls.

2019-05-01 | E-MTAB-6593 | biostudies-arrayexpress