Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide analysis of serum starved prelamin A-accumulating hMSCs gene expression.

ABSTRACT: Analysis of serum starved prelamin A-accumulating hMSCs at gene expression level. The hypothesis tested in the present study was that prelamin A accumulation induces the dysregulation of genes that are essensial for cell survival under a stress condition such as serum starvation. The results provide important information about these genes and the functional categories that are dysregulated due to prelamin A accumulation in serum starved hMSCs. Two samples are analyzed in this microarray experiment: human mesenchymal stem cell cultured under serum starvation conditions (during 24 hours) which accumulate prelamin A (pre-hMSCs) and control mesenchymal stem cells (ctrl-hMSCs). 2 biological replicates (hMSCs derived from 2 different bone marrow donors) and 1 technical replicate are included in this analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Clara Rodriguez

PROVIDER: E-GEOD-52563 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Prelamin A accumulation and stress conditions induce impaired Oct-1 activity and autophagy in prematurely aged human mesenchymal stem cell.

Infante Arantza A Gago Andrea A de Eguino Garbiñe Ruiz GR Calvo-Fernández Teresa T Gómez-Vallejo Vanessa V Llop Jordi J Schlangen Karin K Fullaondo Ane A Aransay Ana M AM Martín Abraham A Rodríguez Clara I CI

Aging 20140401 4

Aging, a time-dependent functional decline of biological processes, is the primary risk factor in developing diseases such as cancer, cardiovascular or degenerative diseases. There is a real need to understand the human aging process in order to increase the length of disease-free life, also known as "health span". Accumulation of progerin and prelamin A are the hallmark of a group of premature aging diseases but have also been found during normal cellular aging strongly suggesting similar mecha ...[more]

PMID: 24753226

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Project description:Expression and differential expression analysis of breast cancer patient samples and normal samples from breast reduction operations. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, LM-CM-8renskog and are referred to as normal tissue. Expression and differential expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850. We analyzed 5 to 6 arrays each for breast cancer patient samples and normal samples.

Dataset Information

Genome-wide analysis of serum starved prelamin A-accumulating hMSCs gene expression.

Publications

Prelamin A accumulation and stress conditions induce impaired Oct-1 activity and autophagy in prematurely aged human mesenchymal stem cell.

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