Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of paired tumour and normal samples from colorectal cancer patients undergoing colonic resection to investigate quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity

ABSTRACT: We investigate the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation using paired tumour and normal samples from colorectal cancer patients undergoing colonic resection.

ORGANISM(S): Homo sapiens

SUBMITTER: Katie Viljoen

PROVIDER: E-MEXP-3715 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity.

Viljoen Katie S KS Blackburn Jonathan M JM

BMC genomics 20130116

<h4>Background</h4>RNA and microarray quality assessment form an integral part of gene expression analysis and, although methods such as the RNA integrity number (RIN) algorithm reliably asses RNA integrity, the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation requires further investigation. We investigated the relationship between RNA integrity and array quality on the commonly used Affymetrix Gene 1.0 ST array ...[more]

PMID: 23324084

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Project description:Macrophage activation during the innate immune response is tightly regulated to prevent tissue damage while activating the defense to cellular attack. Using a mouse model where Trim33 is specifically deleted in mature myeloid cells, we show that TRIM33 is essential for two aspects of the inflammatory response in vivo. Loss of TRIM33 attenuates the initiation of macrophage activation by lipopolysaccharide (LPS) and TRIM33 is necessary to switch off transcription of inflammatory genes during late stages of LPS activation. Using chromatin immunoprecipitation coupled to deep sequencing, we provide a link between TRIM33 binding, RNA Polymerase II occupancy and H3K4me3 spreading on inflammatory genes in macrophages and reveal novel insights concerning the transcriptional regulation of Ifn-beta where TRIM33 exerts a repressive function via a distal regulatory region during late stages of LPS activation of macrophages. These findings pinpoint TRIM33 as a major regulator of the resolution of inflammation and indicate that transcriptional regulators can fine-tune H3K4me3 spreading. To study the role of TRIM33 in the transcriptional response induced by pathogen receptors, we analyzed whether lack of TRIM33 in macrophages affected the TLR-mediated regulation of proinflammatory and antimicrobial genes. To study this role, we bred TRIM33fl/fl mice with Lyz-Cre mice (obtained from The Jackson Laboratory, Bar Harbor, Maine, USA) where the Cre recombinase gene is under the regulatory sequences of the Lyz gene that is expressed only in mature myeloid cells. Bone marrow cells from 2 LyzCre/Trim33+/+ mice and 2 LyzCre/Trim33flox/flox mice were then differentiated in macrophages and treated during 0h, 4h, 12h and 24h with LPS. Total RNA was extracted from macrophages and analysed using cDNA microarrays. The set of gene expression consists of 16 samples of RNA of bone marrow derived macrophages activated with 100ng/ml of LPS during 0h, 4h, 12h, 24h, 8 samples from 2 LyzCre/Trim33+/+ mice and 8 samples from 2 LyzCre/Trim33flox/flox mice.

Dataset Information

Transcription profiling by array of paired tumour and normal samples from colorectal cancer patients undergoing colonic resection to investigate quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity

Publications

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity.

Similar Datasets

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