Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression and differential expression analysis in INA6 cells

ABSTRACT: Expression and differential expression analysis of custom 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. 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 sets 014850. INA6 cells restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. We analyzed three arrays each for INA6 cells after 13 hours of IL-6 withdrawal and cells restimulated with IL-6 for 1 hour

ORGANISM(S): Homo sapiens

SUBMITTER: Kristin Reiche

PROVIDER: E-GEOD-29793 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

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

Expression and differential expression analysis in INA6 cells

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure