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Sample GSM312302 Query DataSets for GSM312302
Status Public on Dec 29, 2008
Title IMR90_alpha_rep4
Sample type RNA
 
Source name Lung fibroblast_irradiated
Organism Homo sapiens
Characteristics primary lung fibroblastTotal RNA
Treatment protocol Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator
Growth protocol Early passage human lung fibroblast cell strain IMR-90 (Coriell repository, NJ) was sub-cultured in Dulbecco’s modified Eagle’s medium (Gibco) and Ham’s F10 medium in a 1:1 mixture plus 15% fetal bovine serum. Young fibroblasts at population doubling <35 were used in all experiments.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Ribopure (Ambion, Applied Biosytems), according to the manufacturer’s instructions
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 g RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions
 
Hybridization protocol 1.5 mg of cRNA (>9 pmol Cy3 per mg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent
Scan protocol Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent)
Description Gene expression after 4hr in 0.5Gy-irradiated human lung fibroblasts
Data processing Background corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Non-uniform outliers or features not significantly above background intensity in 20% or more of the hybridizations were filtered out.
 
Submission date Aug 13, 2008
Last update date Jul 02, 2009
Contact name Shanaz Adi Ghandhi
E-mail(s) shanazg@gmail.com
Phone 212-3053911
Organization name Columbia University Medical Center
Department Center for Radiological Research
Lab VC11-237
Street address 630, W 168th street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL6480
Series (1)
GSE12435 IMR90 4hr bystander experiment 0.5Gy alpha particle strip dish format
Relations
Reanalysis of GSM526645

Data table header descriptions
ID_REF
VALUE BRB ArrayTools, Version 3.7 (NCI) median-normalized log2 transformed signal intensity.

Data table
ID_REF VALUE
GE_BrightCorner 16.56585884
DarkCorner
A_24_P66027 9.0131073
A_32_P77178
A_23_P212522 9.347953796
A_24_P934473
A_24_P9671 14.28517151
A_32_P29551
A_24_P801451 7.323470592
A_32_P30710 15.40299797
A_32_P89523
A_24_P704878
A_32_P86028 14.83568001
A_24_P470079
A_23_P65830 9.140995026
A_23_P109143 13.39837074
A_24_P595567 6.581282616
A_24_P391591 9.209051132
A_24_P799245
A_24_P932757

Total number of rows: 41093

Table truncated, full table size 844 Kbytes.




Supplementary file Size Download File type/resource
GSM312302.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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