Transcriptomics

Dataset Information

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Transcription profiling of human lymphoblastoid cells from patients with limited or acute radiation toxicity, skin cancer patients and normal controls, exposed to UV or IR light


ABSTRACT: Peripheral blood lymphocytes from a total of 57 patients were immortalized with Epstein-Barr virus. Fourteen radiation-therapy patients suffered unusual levels of radiation toxicity (RadS). Thirteen radiation-therapy patients with limited toxicity (RadC) were enrolled as controls. Fifteen patients diagnosed with skin cancer before age 40 (SkCa) were used as a second group of controls. Fifteen healthy subjects without any history of cancer (NoCa) were matched to the skin cancer patients and used as a third group of controls. Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR). For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later. For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later. For example, RadS1-Mock refers to cells from radiation sensitive patient 1 exposed to mock treatment. The published manuscript (PNAS 101:6634, 2004) can be found at http://www.pnas.org/cgi/doi/10.1073/pnas.0307761101; Data were analyzed with Affymetrix MAS version 4.0. Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.

ORGANISM(S): Homo sapiens  

SUBMITTER: Wan-Jen Hong  

PROVIDER: E-GEOD-1725 | ArrayExpress | 2007-08-05

SECONDARY ACCESSION(S): GSE1725GDS968PRJNA90631

REPOSITORIES: GEO, ArrayExpress

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Publications

Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage.

Rieger Kerri E KE   Hong Wan-Jen WJ   Tusher Virginia Goss VG   Tang Jean J   Tibshirani Robert R   Chu Gilbert G  

Proceedings of the National Academy of Sciences of the United States of America 20040419 17


Toxicity from radiation therapy is a grave problem for cancer patients. We hypothesized that some cases of toxicity are associated with abnormal transcriptional responses to radiation. We used microarrays to measure responses to ionizing and UV radiation in lymphoblastoid cells derived from 14 patients with acute radiation toxicity. The analysis used heterogeneity-associated transformation of the data to account for a clinical outcome arising from more than one underlying cause. To compute the r  ...[more]

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