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Sample GSM1057479 Query DataSets for GSM1057479
Status Public on Jun 24, 2013
Title TCD4_7H30_D0025Gy_Ind5
Sample type RNA
 
Source name Lymphocyte TCD4, 450min, 25mGy, Individual5
Organism Homo sapiens
Characteristics cell type: Lymphocyte TCD4
gender: male
Treatment protocol Human whole blood samples from 5 healthy donors were diluted in IMDM medium (1:10) and exposed to 500, 100, 50, 25, 10 and 5 mGy of Cobalt 60 gamma-rays. Gene expression alterations were measured 150, 300, 450 and 600 min post exposure after negative cell sorting of lymphocytes TCD4+ cells.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from lymphocyte T CD4+ using RNeasy Mini columns from the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um double pass, 16 bit Dye channel is set to Green and Green PMT is set to 100%, XDR set to 0.1).
Description Gene expression in Lymphocyte TCD4 450min post-exposure to 25mGy of human whole blood:IMDM (1:10)
Data processing The scanned images were analyzed with Feature Extraction Software 7.5 (Agilent) using default parameters (protocol GE1-107_sep08 and Grid: 026652_D_F_20101031) to obtain raw signal intensities. Microarray raw data were analyzed, normalized and filtered with R software, limma and Agi4x44PreProcess package of the Bioconductor repository. Briefly, the mean signal intensity for each spot was used and a log base 2 transformation was performed. The normalization step was performed using the quantile method of the normalizeBetweenArrays function of the limma package. Agilent Feature Extraction Software flagged undetected spot and bad features allowing excluding them from the analysis. The filtering criteria consisted of removing a probe when it was undetected in at least 75% of the replicates. A total of 19,246 probes were selected after filtering step.
 
Submission date Dec 26, 2012
Last update date Jun 24, 2013
Contact name Gaetan GRUEL
E-mail(s) gaetan.gruel@irsn.fr
Organization name Institut de Radioprotection et de Surete Nucleaire
Department Service de RadioBiologie et d'Epidemiologie
Lab Laboratoire de Dosimetrie Biologique
Street address BP 17
City Fontenay aux Roses Cedex
ZIP/Postal code 92262
Country France
 
Platform ID GPL13497
Series (1)
GSE43151 Characterization of gene expression profiles at low and very low doses of ionizing radiation

Data table header descriptions
ID_REF
VALUE Log base 2 Normalized signal intensity

Data table
ID_REF VALUE
A_23_P42935 7.801
A_23_P117082 9.73
A_23_P2683 7.942
A_24_P358131 7.022
A_32_P14850 14.917
A_23_P158596 7.528
A_23_P350107 11.493
A_23_P388190 8.796
A_23_P106544 10.546
A_32_P85539 8.243
A_23_P94998 7.298
A_23_P103905 10.646
A_24_P497186 8.182
A_23_P434289 6.406
A_33_P3326898 6.901
A_24_P67898 12.663
A_24_P28657 9.088
A_33_P3344292 6.505
A_23_P2873 9.504
A_33_P3223631 8.843

Total number of rows: 19246

Table truncated, full table size 363 Kbytes.




Supplementary file Size Download File type/resource
GSM1057479_252665211931_201011301141_S01_GE1_107_Sep09_1_1.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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