Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HMF3A_RNAi

ABSTRACT: HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen. The pSUPER-retro vector system (Brummelkamp, 2002) was used to selectively target genes for mRNA degradation in an attempt to determine if they had a role, in the changes to the transcriptome upon LT inactivation. The genes chosen for targeting were BTG2, NR4A3, DUSP1, PHLDA1 and STACb. Keywords = LT antigen Keywords = senescence Keywords = fibroblast Keywords = BTG2 Keywords = DUSP1 Keywords = MKP-1 Keywords = NR4A3 Keywords = STAC Keywords = PHLDA1 Keywords = RNAi

ORGANISM(S): Homo sapiens

SUBMITTER: Parmjit Jat

PROVIDER: E-GEOD-690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptional networks and cellular senescence in human mammary fibroblasts.

Hardy K K Mansfield L L Mackay A A Benvenuti S S Ismail S S Arora P P O'Hare M J MJ Jat P S PS

Molecular biology of the cell 20041201 2

Senescence, the molecular program that limits the finite proliferative potential of a cell, acts as an important barrier to protect the body from cancer. Techniques for measuring transcriptome changes and for modulating their expression suggest that it may be possible to dissect the transcriptional networks underlying complex cellular processes. HMF3A cells are conditionally immortalized human mammary fibroblasts that can be induced to undergo coordinated senescence. Here, we used these cells in ...[more]

PMID: 15574883

Similar Datasets

HMF3A_RNAi

2004-03-01 | GSE690 | GEO

HMF3A_with_3Dwt

Project description:HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen. HMF3A cells cease proliferating by 4 days at 39Â°C. We directly compared the gene expression profiles of cells at 33.5Â°C and after shift up to 39.5Â°C for 7 days (10 arrays, 3 biological replicates). To eliminate genes that change in response to the temperature shift, we compared the profiles of HMF3Dwt cells at 33Â°C and those shifted up to 39Â°C for 7 days (4 arrays, 2 biological replicates). Since HMF3Dwt cells were immortalised with wild type U19 LT antigen, they proliferate at both temperatures. To break up the list of genes obtained with the 7 day shift, we performed several further comparisons on the arrays. HMF3A cells at 33Â°C were compared to the primary donor fibroblasts (HMF3 passage 8, 4 arrays), HMF3A cells shifted to 39Â°C for 2 days (4 arrays, 2 biological repeats), HMF3A cells shifted to 39Â°C for 7 days and then shifted back to 33Â°C for 3 days (8 arrays, 4 biological repeats) or 7 days (4 arrays, 2 biological repeats). As a comparison to the irreversible process of senescence, we sought to identify genes that changed upon reversible growth arrest, quiescence. Thus changes that occurred when the cells were grown to confluency and starved were also determined (2 biological replicate, 6 arrays). Keywords = Rb Keywords = fibroblast Keywords = immortalization Keywords = LT antigen Keywords = p53 Keywords = quiescence Keywords = senescence

2010-06-09 | E-GEOD-688 | biostudies-arrayexpress

GSEp53_v_Con

2010-06-09 | E-GEOD-689 | biostudies-arrayexpress

The effect of Ras on the signalling networks in senescence

Project description:Activated Ha-ras was introduced to HMF3A cells. HMF3A cells are conditionally immortalised human mammary fibroblasts. They undergo co-ordinated senescence upon inactivation of LT antigen, when cultured at 39C. The introduction of Ras did not prevent this but affected the molecular profile. Keywords = Senescence Keywords = fibroblast Keywords = Ras Keywords = immortalization Keywords = transformation

2010-06-09 | E-GEOD-979 | biostudies-arrayexpress

Diff_cell_shift

Project description:Immortalised lines created from different cell types from the human breast were induced to undergo senesecence by inactivation of the immortalising LT antigen.

2010-06-10 | E-GEOD-2427 | biostudies-arrayexpress

Prim_Fibs

Project description:To determine changes in gene expression in primary fibroblasts undergoing replicative senescence, a direct comparison between early passage proliferating cells and senescent cells was performed. Frozen stocks of the primary fibroblasts (HMF3) from which the lines HMF3A and HMF3Dwt were derived (O'Hare, PNAS:98, 2001) were serially passaged twice through to senescence to yield 2 independent sets of RNA. A third set of RNA was from a different female donor (F1068). The three different sets of RNA were put on 4 arrays each. Data is also provided for F1068 fibroblasts at late passage. Keywords = fibroblast Keywords = senescence Keywords = breast

2010-06-09 | E-GEOD-687 | biostudies-arrayexpress

Identification of RNAs that are physically and functionally associated with RNase P

Project description:Numerous RNAs copurify with RNase P and are affected by temperture sensitive mutations in conserved residues with the essential RNA and protein subunits. Specifically, RNase P physically interacts with ribosomal protein mRNAS and the intron-encoded box C/D snoRNAs. Keywords: RNA copurification, temperature sensitive mutants ORF and intergenic regions were analyzed in order to determine which RNAs were affected in RNase P strains.

2008-06-01 | E-GEOD-10514 | biostudies-arrayexpress

Reduced atherosclerosis in MyD88 null mice

Project description:This series represents a comparison of gene expression in mouse aorta from MyD88-/-, apoE-/- mice versus apoE-/- control mice fed a high fat diet for 8 weeks, causing atherosclerotic lesion development. 5 MyD88-/-, apoE-/- mice were compared to 5 apoE-/- control mice and dye swap replicated for a total of 10 replicate microarrays. Keywords = Mus musculus Keywords = aorta Keywords = atherosclerosis Keywords = MyD88

2010-06-09 | E-GEOD-1058 | biostudies-arrayexpress

Golden-mantled ground squirrel (Spermophilus lateralis) hibernating liver transcriptome

Project description:This series represents the liver transcriptome for animals sampled during summer, interbout arousal, and late torpor Keywords = squirrel Keywords = liver Keywords = hibernation

2010-06-05 | E-GEOD-2024 | biostudies-arrayexpress

Changes in genome-wide occupancy of core transcriptional regulators during stress

Project description:Organisms respond to heat stress by reprogramming gene expression. Here we show that genome-wide reprogramming involves enhanced assembly of the TFIID and SAGA regulatory pathways at heat induced genes, and disassembly of the TFIID pathway at heat-repressed genes. While TFIID and SAGA are recruited to heat-induced genes, only SAGA appears to be associated with achieving maximal induction. Mot1, an ATP-dependent inhibitor of the TATA binding protein TBP, assembles at heat-induced SAGA-regulated genes, but functions to attenuate rather than promote activation. Changes in promoter occupancy of bromodomain factor Bdf1 are tightly linked to changes in TFIID occupancy, which further supports the notion that the two work together. Bdf1 is inhibitory to a number of SAGA-regulated genes and dissociates when these genes are activated, suggesting that Bdf1 normally blocks transcription complex assembly at these genes. These linkages in reprogramming of factor occupancy at promoters provide direct evidence for two functionally distinct transcription assembly pathways, and reveal unexpected cross-talk between the pathways. Keywords = Chromatin Immunoprecipitation Keywords = Microarray Keywords = TBP

2010-06-05 | E-GEOD-1373 | 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