Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq analysis of Huh7 cells upon stable-knockdown of L1 elements

ABSTRACT: L1 elements are repeat elements known to get activated during hepatocarcinogenesis. We have knocked-down expression of L1 elements using shRNA targeting L1-ORF1 in Huh7 cell line and a control non-targeting cell line was also generated. Influence of L1 knockdown on overall cellular transcritome was then analysed by RNAseq followed by pathway analysis. Overall, a crosstalk between L1 elements and TGFbeta signaling pathway is observed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE126615 | GEO | 2023/01/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of MCF-7 (breast adenocarcinoma) and 2102Ep (embryonic carcinoma) cells upon LINE-1 knockdown.

Project description:To measure the levels of expression of retrotransposon individual copies, and particularly of LINE-1 (L1) elements of the L1HS-Ta subfamily, we performed 2x150 bp paired-end and strand-specific RNA-seq on polyA+ RNA of MCF-7 and 2102Ep cells, which express high levels of L1. To confirm the origin of the L1-specific signal, we also performed RNA-seq upon shRNA-mediated L1 knockdown. sh960 relates to a scramble shRNA control. sh1083 and sh1085 relate to two distinct shRNAs directed against the ORF1 region of L1.3 (GenBank L19088) as a prototype L1HS-Ta.

2016-05-25 | E-MTAB-3788 | biostudies-arrayexpress

RNAseq analysis of Hep3B cells upon overexpression of LINE1 retrotransposon encoded protein L1orf1p

Project description:L1 retrotransposons are known to get activated during hepatocarcinogenesis. We have developed inducible (TET-ON) overexpression of L1orf1 using piggybac vector in Hep3B cell line and a control TET-ON-empty cell line was also generated. Influence of L1orf1 overexpression on overall cellular transcritome was then analysed by RNAseq followed by pathway analysis. Overall, a number of key oncogeneic pathways are dysregulated upon L1orf1 overexpression is observed.

2023-01-21 | GSE194251 | GEO

Human LINE-1 ORF1p complex LC-MS/MS

Project description:Host proteins regulate LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles.

2023-03-11 | PXD038851 | Pride

Host Factors with Reduced Expression in Two HCV Permissive Cell Lines as Compared to the Non-Permissive Parent Cell Line Huh7

Project description:Drugs directly targeting Hepatitis C (HCV) are often rendered useless by the high mutation rate of the virus. Thus, we deduce that targeting of host factor that affect HCV replication may provide enhanced therapy fort HCV infection. Hepatocyte cell line Huh7 is known to be non-permissive for Hepatits C (HCV) replication. Through a method developed by the Rice laboratory (Blight, K.J., et al., J Virol, 2002), selection of a small subset of permissive hepatocytes is possible. The Rice laboratory generated the first permissive cell line, Huh7.5, using this method. We generated another permissive cell line, HRP1, using the same method. With microarray, we compared the expression of host mRNAs in non-permissive Huh7 to both Huh7.5 and HRP1 searching for host factors lost in the cell lines permisive for HCV replication. Non-permissive cell line Huh7 and permissive cell lines Huh7.5 and HRP1 were harvested for RNA extraction and hybridization on Affymetrix microarrays.

2011-05-01 | E-GEOD-25156 | biostudies-arrayexpress

Transcription profiling of human hepatocellular carincoma-derived cell line Huh7-S33Y with high TCF activity compared to a control Huh7 cell line

Project description:The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. Β-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ β-catenin signaling. The aim of this study was to identify novel genes that are regulated by active β-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low β-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) β-catenin/TCF activity clones, those had been xenografted into nude mice. We compared and contrasted SAGE and genome-wide microarray data, in parallel. Finally; after combined analysis, we identified BRI3 and HSF2 as novel targets of Wnt/β-catenin signaling in hepatocellular carcinoma. Experiment Overall Design: High TCF activity Huh7 cell line (Huh7-S33Y) was compared to control Huh7 cell line (Huh7-Vec) by using 10 ug of total RNA isolated from each sample (15 ug of labeled cRNA was hybridized to the arrays). Triplicates are coming from same total RNA extraction.

2009-10-10 | E-GEOD-11916 | biostudies-arrayexpress

Host Factors with Reduced Expression in Two HCV Permissive Cell Lines as Compared to the Non-Permissive Parent Cell Line Huh7

2011-05-01 | GSE25156 | GEO

DNA microarray analysis of Huh7 and JMJD5KO Huh7 cells.

Project description:To understand the roles of JMJD5 in liver cells, we performed DNA microarray analysis by using JMJD5KO Huh7 cells. We noticed that several transcriptional factors involved in differentiation to hepatocytes were down-regulated in JMJD5KO Huh7 cells compared to parent Huh7 cells..

2016-01-23 | GSE73491 | GEO

Gene expression analysis of Huh7 cells treated with human or mouse erythroferrone (ERFE)

Project description:Analysis of overall gene expression changes in Huh7 cells after treatment with mouse or human erythroferrone (ERFE)

2018-08-10 | GSE118367 | GEO

Comparison of TCF hyper-activated and control Huh7 cells - SAGE

Project description:The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. ?-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ ?-catenin signaling. The aim of this study was to identify novel genes that are regulated by active ?-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low ?-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) ?-catenin/TCF activity clones, those had been xenografted into nude mice. We compared and contrasted SAGE and genome-wide microarray data, in parallel. Finally; after combined analysis, we identified BRI3 and HSF2 as novel targets of Wnt/?-catenin signaling in hepatocellular carcinoma. High TCF activity Huh7 cell line (Huh7-S33Y) was compared to control Huh7 cell line (Huh7-Vec) by using 25 ug of total RNA isolated from each sample

2009-09-30 | E-GEOD-11912 | biostudies-arrayexpress

Gene expression analysis of different passages and subclones of the Huh7 cell line

Project description:Hepatitis C Virus (HCV) has a extremely narrow host cell tropism and robustly infects only very few cell lines, most importantly the human hepatoma cell line Huh7. This cell line was isolated from a 57-year old Japanese male with fulminant hepatitis. Different subclones and passages of the Huh7 cell line show up to 1000-fold differences in HCV replication efficiency (permissiveness). In this experiment, we sought to identify factors responsible for these differences by correlating gene expression from eight different uninfected Huh7 variants with their respective HCV permissiveness. HCV replication efficiency was determined using electroporation of a subgenomic luciferase reporter replicon (genotype 1b, "con1/ET") and measuring luciferase activity at 48h post transfection normalized to the input value at 4h p.t.. "Relative permissiveness" of cell lines corresponds to their replication efficiency, normalized to the efficiency in the lowest permissive cells (Huh7 p13 and p28).

2019-11-08 | GSE140114 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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