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Sample GSM316365 Query DataSets for GSM316365
Status Public on Apr 06, 2009
Title GM12804-0hr
Sample type RNA
 
Source name Lymphoblastoid cell line, 0hr
Organism Homo sapiens
Characteristics coriell cell line: GM12804
cell type: lymphoblastoid cells
ceph id: 1454.4
relationship: daughter
treatment: none
treatment time: 0hr
Biomaterial provider Corriell Cell Repositories; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12804
Treatment protocol 10 Gy of ionizing radiation (IR) in a 137Cs irradiator.
Growth protocol The cells were grown at a density of 500,000 cells/ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy Mini-Kit (Qiagen) as per the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion/Applied Biosystems) from 1 microg of total RNA following manufacturer's instructions.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human U133A 2.0 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Baseline, GM12804

Gene expression data from lymphoblastoid cells prior to irradiation.
Data processing The data were analyzed with Expression Console software using the MAS5 probe summary method and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Aug 29, 2008
Last update date Sep 19, 2011
Contact name Michael Patrick Morley
E-mail(s) mmorley@pennmedicine.upenn.edu
Phone 215-898-2026
Organization name Perelman School of Medicine at the University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL571
Series (2)
GSE12626 Genetic analysis of radiation-induced changes in human gene expression
GSE26835 Genetic variation in radiation-induced cell death

Data table header descriptions
ID_REF
VALUE Log2 transformed Expression Console-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P) or absent (A)

Data table
ID_REF VALUE ABS_CALL
1007_s_at 7.90014890369911 P
1053_at 9.53030683745829 P
117_at 7.24690112649153 P
121_at 9.15439207145875 P
1255_g_at 5.00099872054872 A
1294_at 7.83516805250959 P
1316_at 5.82814257873454 A
1320_at 2.39790205819429 A
1405_i_at 10.3751741345349 P
1431_at 4.91230160264848 A
1438_at 4.89126022887152 A
1487_at 8.69965781527901 P
1494_f_at 6.50793779283491 A
1598_g_at 7.44584255388934 A
160020_at 8.08675086532386 P
1729_at 7.59822970807511 P
1773_at 6.27255252816289 A
177_at 7.47668140775974 P
179_at 8.00127588263418 A
1861_at 7.42961680103156 P

Total number of rows: 22277

Table truncated, full table size 649 Kbytes.




Supplementary file Size Download File type/resource
GSM316365.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM316365.CHP.gz 203.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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