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Sample GSM905912 Query DataSets for GSM905912
Status Public on Mar 28, 2013
Title irStress_95unrelated_GM06990_2hr
Sample type RNA
 
Source name Lymphoblastoid cell lines derived from GM06990
Organism Homo sapiens
Characteristics cell line: GM06990
treatment: 10 Gy ionizing radiation
time: 2hr
Biomaterial provider Corriell: GM06990 http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
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 7G.
Description Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator from GM06990 2 hours after exposure.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Mar 28, 2012
Last update date Mar 28, 2013
Contact name Renuka Nayak
Organization name HHMI, University of Pennsylvania
Street address 3516 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL571
Series (1)
GSE36910 Gene expression levels in immortalized B cells from 95 unrelated CEPH-Utah individuals treated with 10Gy of ionizing radiation

Data table header descriptions
ID_REF
VALUE Log2 transformed MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)

Data table
ID_REF VALUE ABS_CALL
1007_s_at 8.17821915246567 P
1053_at 9.80138131097369 P
117_at 5.52499359076453 P
121_at 9.36622450113636 P
1255_g_at 4.15554524656194 A
1294_at 8.25879967268158 P
1316_at 4.67005794653634 A
1320_at 5.05434578989271 A
1405_i_at 10.6824495211069 P
1431_at 4.53908745023363 A
1438_at 4.40724124730868 A
1487_at 8.28020703477169 P
1494_f_at 6.56419538106111 P
1598_g_at 7.31515680968571 A
160020_at 7.02384082925766 A
1729_at 8.83357639652722 P
1773_at 6.76651433250186 A
177_at 4.73658485277601 A
179_at 8.91761524335933 A
1861_at 8.18043284247668 P

Total number of rows: 22277

Table truncated, full table size 649 Kbytes.




Supplementary file Size Download File type/resource
GSM905912_GM06990_2hr.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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