Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HCV Replication: permissive and non-permissive cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Qiuyue Chen

PROVIDER: E-GEOD-31962 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis.

Yang Ivana V IV Coldren Christopher D CD Leach Sonia M SM Seibold Max A MA Murphy Elissa E Lin Jia J Rosen Rachel R Neidermyer Amanda J AJ McKean David F DF Groshong Steve D SD Cool Carlyne C Cosgrove Gregory P GP Lynch David A DA Brown Kevin K KK Schwarz Marvin I MI Fingerlin Tasha E TE Schwartz David A DA

Thorax 20130619 12

<h4>Background</h4>Idiopathic pulmonary fibrosis (IPF) is an untreatable lung disease with a median survival of only 3-5 years that is diagnosed using a combination of clinical, radiographic and pathologic criteria. Histologically, IPF is characterised by usual interstitial pneumonia (UIP), a fibrosing interstitial pneumonia with a pattern of heterogeneous, subpleural regions of fibrotic and remodelled lung. We hypothesised that gene expression profiles of lung tissue may identify molecular subt ...[more]

PMID: 23783374

Similar Datasets

Huh7 cells exist as a mixed population of cells with distinct patterns of gene methylation

Project description:A powerful approach to study innate antiviral response is to compare the difference between wild type Huh7 cells, which do not support robust replication of hepatitis C virus (HCV)2, versus certain subclones of Huh7 cells that are permissive for HCV replication. We generated two permissive cell lines and two independent non-permissive subclone from Huh7 cells. We compared the global methylation pattern of these different cells and find that Huh7 cells exist as a heterogeneous population of cells with distinct patterns of gene methylation. Comparison of Huh7, HRP1, HRP4, Huh7-pNeo1 and Huh7-pNeo2 cells.

2013-07-03 | E-GEOD-31960 | biostudies-arrayexpress

MX1 is Silenced in Permissive HRP4 Cells Supporting HCV Replication

Project description:MX1 is a well-characterized interferon-induced antiviral gene. MX1 is activated by viral infection due to interferon production in cells. We treated non-permissive Huh7 cells and permissive HRP4 cells with interferon. We compared the expression of genes induced by interferon to determine host factors affecting HCV replication. Huh7 cells and HRP4 cells were treated with 40U/ml interferon-Î± for 6h. RNA was extracted and hybridized on Affymetrix microarrays

2013-07-03 | E-GEOD-31903 | biostudies-arrayexpress

RNA-seq of human liver cancer cell lines after lncRNA overexpression with CRISPRa

Project description:Biological replicates of Human liver cancer cell line Huh7 (n = 2-4) were treated with CRISPRa to overexpress (OE) LINC00326, LINC01419, LINC02119, novel lncRNAs MSTRG.12891, as well as and non-targeting (NT) control. Cells were harvested 48hrs after transfection. Total RNA was extracted and sequenced with a strand-specific paired end RNA-seq protocol.

2021-12-23 | E-MTAB-9586 | biostudies-arrayexpress

HBV remodels PP2A complexes to rewire kinase signaling in hepatocellular carcinoma

Project description:Hepatitis B virus (HBV) infection promotes liver cancer initiation by inducing inflammation and cellular stress, but its impact in established tumors is not well understood. We used affinity purification mass spectrometry to comprehensively map a network of 145 physical interactions between HBV and human proteins in hepatocellular carcinoma (HCC). A subset of the host factors targeted by HBV proteins are preferentially mutated in non-HB¬V-associated HCC suggesting that their interaction with HBV influences HCC biology. These include proteins involved in mRNA splicing, mitogenic signaling and DNA repair, with the latter set interacting with the HBV oncoprotein X (HBx). We show that HBx remodels the PP2A phosphatase complex by excluding striatin regulatory subunits from the PP2A holoenzyme. We find that HBx effects on PP2A cause Hippo kinase activation, particularly in cells with high striatin levels. In parallel, HBx activates mTOR complex 2 (mTORC2) to prevent YAP degradation. mTORC2 effects on YAP can be observed in human HCC specimens and mouse HCC models and can be targeted with mTOR kinase inhibitors. Thus, HBV interaction with host proteins rewires HCC signaling rather than directly activating mitogenic pathways. These findings provide a new paradigm for the cellular effects of a tumor promoting virus and support a model where HBV may have therapeutic actionable effects on HCC biology.

2024-11-23 | PXD055366 | Pride

M12-28: MRX34 Biomarker study in animals bearing HuH7 orthotopic liver tumors [Affymetrix]

Project description:To identify direct tumor mRNA targets of miR-34a, tumor RNAs isolated from whole tumors from animals treated with negative control and MRX34 HuH7 cells were surgically implanted into the livers of Nod/Scid mice and allow to grow for multiple weeks. Once serum AFP levels reached levels consistent with tumor growth of ~80-100 mg, animals were subjected to a single IV injection of MRX34. Twenty-four hours later animals were sacrificed, tumors resected and RNA isolated for subsequent microarray analysis.

2014-11-05 | E-GEOD-58800 | biostudies-arrayexpress

Study of microRNA associated with cisplatin's anti-tumor effect in hepatocellular carcinoma

Project description:The miRNAs expression was markedly altered with the treatment of cisplatin in vitro and various miRNAs induced by cisplatin also may contribute to tumor growth in vitro. Using a custom microarray platform, we analyzed the expression levels of 1719 human miRNA probes in the cell lines in vitro that were treated with and without cisplatin.

2016-03-15 | E-GEOD-55806 | biostudies-arrayexpress

MRX34 Biomarker study in animals bearing Hep3B orthotopic liver tumors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-05 | E-GEOD-58893 | biostudies-arrayexpress

Study of microRNA associated with metforminM-bM-^@M-^Ys anti-tumor effect [Huh7 cells]

Project description:The miRNAs expression was markedly altered with the treatment of metformin in vitro and in vivo and various miRNAs induced by metformin also may contribute to tumor growth in vitro and in vivo. Using a custom microarray platform, we analyzed the expression levels of 985 human miRNA probes in the cell lines in vitro and tumorous tissues in vivo that were treated with and without metformin.

2015-03-01 | E-GEOD-44204 | biostudies-arrayexpress

Gene expression profiling of histone deacetylase inhibition in epithelioid sarcoma

Project description:Epithelioid Sarcoma (ES) is a rare neoplasm uniquely comprised of cells exhibiting both mesenchymal and epithelial features. Having propensity for local and distant recurrence, it can pose a diagnostic dilemma secondary to pathologic complexity. Patients have dismal prognosis due to lack of effective therapy. HDAC inhibitors exhibit marked anti-tumor effects in various malignancies. Our studies demonstrate that pan-HDAC inhibitors constitute potentially novel therapeutics versus ES. Human ES cells (VAESBJ, HS-ES, Epi544) were studied in vitro to evaluate the effects of HDACi. Gene array analysis was used to identify the impact of HDACi on ES gene expression in three cell lines.

2015-11-03 | E-GEOD-66800 | biostudies-arrayexpress

Expression data comparing Huh7 control and CD47 knockdown cells

Project description:To identify candidate genes regulated by CD47 Affymetrix Human Genome U133 Plus GeneChip 2.0 HCC cell line Huh7 cells with or without CD47 repressed

2014-06-01 | E-GEOD-47563 | 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