Diff_cell_shift
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Parmjit Jat
PROVIDER: E-GEOD-2427 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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 39°C. We directly compared the gene expression profiles of cells at 33.5°C and after shift up to 39.5°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 33°C and those shifted up to 39°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 33°C were compared to the primary donor fibroblasts (HMF3 passage 8, 4 arrays), HMF3A cells shifted to 39°C for 2 days (4 arrays, 2 biological repeats), HMF3A cells shifted to 39°C for 7 days and then shifted back to 33°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
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. 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
2010-06-09 | E-GEOD-690 | biostudies-arrayexpress
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. Given the importance of p53, we sought to determine what gene changes were affected if its activation was inhibited. To do this we used the Genetic Suppressor Element (GSE)56 which inhibits the transcriptional activity of p53 (Ossovskaya, 1996). The presence of the GSEp53 delayed the arrest of the HMF3A cells when LT was inactivated. However the cells did arrest. We thus examined the array profiles for 3A-GSEp53 cells after 2 and 7 days of LT inactivation (against 3A-GSEp53 cells at 33°C) and compared these to the profiles for 3A-puro cells. Keywords = p53 Keywords = LT antigen Keywords = fibroblast Keywords = senescence Keywords = Rb
2010-06-09 | E-GEOD-689 | biostudies-arrayexpress
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
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
Project description:The expression profiles of Drosophila Kc167 and SL2 cells were compared on the CDMC_Drosophila_7k2 array platform. Three independent RNA samples from each cell line were isolated and compared in a pairwise fashion. Dye-flip experiments were also performed. See Neal et al. 2003 for results and discussion. Keywords = Kc167 Keywords = SL2 Keywords = Drosophila
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Project description:Epithelial cells were in contact either with live bacteria (S. aureus) or with bacterial supernatant during 3 hours. Three dependant experiment for each condition were performed. RNA from epithelial cells were extracted. Each condition was hybridized on 6 slides (3 slides with their corresponding swap)
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Project description:Genomic and behavioral investigations were performed to determine the effects of a mutation in a Drosophila soluble guanylyl cyclase gene. A mutant DGCalpha1[3] third chromosome was crossed into a natural rover (for[R]) or natural sitter (for[s]) genetic background. (See Osborne et al. 1997; PMID: 9242616.) First instar larvae were collected and grown on 60mm Petri plates containing 10 mL of food until mid-third instar. (Approximate density was 3 animals per mL food). Larvae were collected and washed quickly with distilled water and were flash frozen in liquid nitrogen. Co-reared larvae were tested for behavioural effects. Four independent collections were made for each of the two conditions (Rover_DGCalpha1[3] or sitter_DGCalpha1[3]). Keywords = Drosophila Keywords = foraging Keywords = behavior Keywords = cGMP Keywords = guanylyl cyclase Keywords = genetic background
2010-06-10 | E-GEOD-2136 | biostudies-arrayexpress
Project description:Wildtype and SIPK -silenced (RNAi) tobacco cell suspension cultures were grown in MS medium at 25 C in the dark. Cell suspension cultures were transferred to fresh growth medium 3 days prior to pooling each genotype and dividing the pool into 3 x 10ml volumes per genotype. A 30 minute pre-incubation was used with xanthine (for abiotic controls and treatments), but no pre-treatment was used for the biotic stressors. For each treatment and abiotic/biotic controls, the cells were harvested by vacuum filtration at the appropriate time points (controls sampled at 0 hrs) and frozen in N2(l) for RNA extraction. In order to discern the effect of silencing SIPK on the transciptome in defence response, biological replicates of WT and SIPK-Ri were randomly paired on 3 slides per treatment or control group. Series_weblink: http://www.tigr.org/tdb/potato Keywords = potato, Biotic stress
2010-06-10 | E-GEOD-2675 | biostudies-arrayexpress
Project description:A large batch of Drosophila Kc167 total RNA was prepared and was used for 3 homotypic hybridizations in order to evaluate the inter-slide variability using the CDMC_Drosophila_7k2 platform. See Neal et al. 2003 for results and discussion. Keywords = Kc167 Keywords = Drosophila Keywords = Platform Variability
2010-06-05 | E-GEOD-418 | biostudies-arrayexpress