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Sample GSM29791 Query DataSets for GSM29791
Status Public on Sep 06, 2004
Title NoCa3-UV
Sample type RNA
 
Source name Lymphoblastoid cells immortalized with Epstein-Barr virus
Organism Homo sapiens
Extracted molecule total RNA
 
Description 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.

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.
Keywords = Gene expression in lymphoid cells of cancer patients
 
Submission date Sep 01, 2004
Last update date Mar 16, 2009
Contact name Wan-Jen Hong
E-mail(s) [email protected]
Phone 650-725-6441
Organization name Stanford University School of Medicine
Department Medicine/Biochemistry
Lab Gilbert Chu
Street address 269 Campus Dr., CCSR Room 1140
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL8300
Series (2)
GSE1725 Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage
GSE1977 Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells

Data table header descriptions
ID_REF
SIGNAL_RAW Signal intensity values from Affymetrix MAS 4.0 prior to normalization
VALUE Normalized values of signal intensity as a measurement of gene expression
ABS_CALL Present/Absent/Marginal call as determined in Affymetrix MAS 4.0

Data table
ID_REF SIGNAL_RAW VALUE ABS_CALL
AFFX-MurIL2_at -16 -12.29 A
AFFX-MurIL10_at 46 48.58 A
AFFX-MurIL4_at -2.7 -1.76 A
AFFX-MurFAS_at 64.5 67.22 A
AFFX-BioB-5_at 55.9 58.57 A
AFFX-BioB-M_at 57.2 59.88 A
AFFX-BioB-3_at 11.1 12.63 A
AFFX-BioC-5_at 570.3 560.66 P
AFFX-BioC-3_at 443.7 438.30 P
AFFX-BioDn-5_at 294.4 293.38 P
AFFX-BioDn-3_at 1400.4 1357.19 P
AFFX-CreX-5_at 6640.3 6329.03 P
AFFX-CreX-3_at 7701.2 7331.50 P
AFFX-BioB-5_st -33 -14.92 A
AFFX-BioB-M_st 69.5 76.63 A
AFFX-BioB-3_st -212.2 -182.31 A
AFFX-BioC-5_st -421.6 -368.19 A
AFFX-BioC-3_st -80 -66.64 A
AFFX-BioDn-5_st 13.9 15.59 A
AFFX-BioDn-3_st 167.1 168.90 P

Total number of rows: 12625

Table truncated, full table size 291 Kbytes.




Supplementary data files not provided

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