Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human hepatocellular carcinoma (HCC) patients

ABSTRACT: Tumor samples and matching healthy tissue from 23 human hepatocellular carcinoma (HCC) patients and one hepatocellular adenoma patient were collected after surgical resection. Total RNA was harvested and sequenced with a strand-specific single-end RNA-seq protocol.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Claudia Kutter

PROVIDER: E-MTAB-8915 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Dietary cholesterol promotes fatty liver-associated liver cancer by inducing aberrant genomic expression and mutations

Project description:We investigated the effects of cholesterol on nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) in diethylnitrosamine-injected mice fed high-fat high-cholesterol (HFHC) diet versus high-fat (HF) alone. mRNA microarray analysis was applied for expressional aberrations.

2018-09-27 | E-MTAB-6002 | biostudies-arrayexpress

Post-transplant (non-alcoholic steatohepatitis) NASH compared with transplanted normal controls

Project description:Non-alcoholic fatty liver disease (NAFLD) encompasses a spectrum of disease that ranges from simple steatosis, to inflammatory form non-alcoholic steatohepatitis (NASH), cirrhosis, and up to hepatocellular carcinoma. While NASH usually takes decades to develop at a rate of one stage per seven years, in the case of post-trasplant NASH (pt-NASH) develops fibrosis much more rapidly, with almost 50% of liver transplant recipients presenting stage 3 fibrosis by 5 years post-transplant. Archived fresh-frozen transplanted liver biopsy samples from four liver biopsy samples with evidence of NASH (2 recurrent and 2 de novo), two with simple steatosis (both de novo), and five with normal histology as controls had their transcriptome sequenced in two batches for deeper coverage.

2022-05-09 | E-MTAB-11688 | biostudies-arrayexpress

miRNA and mRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus

Project description:This SuperSeries is composed of the following subset Series: GSE35402: miRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus GSE35403: mRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus Refer to individual Series

2012-07-02 | E-GEOD-35404 | biostudies-arrayexpress

Transcription profiling of mouse liver cells with liver specific deletion of Irs1 and/or Irs2 and Foxo1during fasting and feeding

Project description:The effect of liver specific deletion of the insulin receptor substrate-1 (Irs1) and/or Irs2 upon gene expression in the fasted and fed liver of mice; and the effect of liver specific Foxo1 deletion in the Irs1 and Irs2 knockout liver during fasting and feeding.

2008-07-31 | E-MEXP-1649 | biostudies-arrayexpress

Transcription profiling of dab hepatocellular adenoma liver tumours (Limanda limanda)

Project description:A custome-made 8x15k oligonucleotide limanda limanda microarray (Agilent) comprised of 14919 experimental probes, was used to characterize gene expression profiles of dab hepatocellular adenoma tumours from sites of different pollution status in Irish Sea.

2011-11-04 | E-MTAB-734 | biostudies-arrayexpress

ChIP-chip by array of zebra fish hepatocellular carcinoma and normal liver to detect differences in CG island methylation

Project description:The aim of the experiment was to detect differences in CG island methylation between hepatocellular carcinoma and normal liver in zebrafish. Zebrafish were treated with DMBA, producing hepatocellular carcinoma, genomic DNA was prepared from these and control zebrafish livers. Methylated DNA was immunoprecipitated from HCC and control samples and labeled with Cy5, samples were co-hybridised with Cy3 labeled zebrafish genomic DNA to the Birmingham D. rerio Agilent 025794 45220 v1 microarray.

2011-01-01 | E-MTAB-209 | biostudies-arrayexpress

cDNA microarray of hepatocellular carcinoma and nontumor liver tissues

Project description:In order to identify the deregulated genes in hepatocellular carcinama, we applied the Agilent two-color chip cDNA microarray to explore the expression of genes in hepatocellular carcinoma and nontumor liver tissue samples. Hepatocellular carcinoma tissues and nontumor liver tissues were obtained from hepatocellular carcinoma patients during surgery. In these samples, RNA was extracted and cDNA microarray was performed to identify the differentially expressed genes in these samples. Hepatocellular carcinoma tissues and nontumor liver tissues were obtained from hepatocellular carcinoma patients during surgery. We included four hepatocellular carcinoma patients in this study, and there are four nontumor tissues and four hepatocellular carcinoma tissues.

2011-12-23 | E-GEOD-34674 | biostudies-arrayexpress

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

Project description:Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether unwanted plasticity is actively suppressed by lineage-specific repressors. Here, we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that Prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternate fate master regulators. In line with patient data, PROX1 overexpression in mice blocked initiation and progression of hepatocellular carcinoma and extended survival. Remarkably, Prox1 depletion caused hepatocyte fate loss in vitro, and promoted transdifferentiation of hepatocellular- to cholangio-carcinoma in vivo. Our findings provide mechanistic evidence for PROX1 as a hepatocyte-specific safeguard and support a model where individual cell type-specific repressors actively suppress plasticity throughout life to safeguard lineage choice and prevent disease.

2024-11-11 | PXD053043 | Pride

Affymetrix on human colon cancer cell line GP5d with siRNA against CTNNB1, MAX and MXD1 against control siRNA

Project description:To find target genes of MYC in GP5d human colon cancer cells, the cells were treated with siRNA against CTNNB1 and MAX. The level of MYC knockdown in human was not sufficiently efficient to be included in the experiments within the criteria list, and hence the values from CTNNB1 knockdown were used as the expression MYC dropped to below 5% of that in the control sample in RNAseq.

2022-04-26 | E-MTAB-9322 | biostudies-arrayexpress

Analysis of RNA from liver tumors in SRSF3 hepatocyte knockout mice

Project description:RNA from three hepatocellular carcinomas from 24-month-old SRSF3HKO mice compared to RNA from non-tumorous liver from 24-month-old SRSF3HKO mice for changes in exon utilization and gene expression. Liver tumor vs. normal liver, three replicates each.

2015-05-01 | E-GEOD-57019 | biostudies-arrayexpress

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