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Sample GSM460679 Query DataSets for GSM460679
Status Public on Oct 09, 2009
Title HepG2 hypoxia (0.5%O2) treatment 12h, biological rep2
Sample type RNA
 
Source name HepG2 hypoxia (0.5%O2) treatment 12h, biological rep2
Organism Homo sapiens
Characteristics cell line: HepG2 hepatoma
stress: hypoxia
time: 12h
Treatment protocol HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells were collected under normoxic conditions (~19% O2, 0 hours) and after 4, 8 and 12 hours of hypoxia treatment (0.5% O2).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
 
Hybridization protocol Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
Scan protocol Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
Description HepG2_H12-2
Data processing We used GcRMA module on Bioconductor with most updated custom CDF (CDF: Hs133P_Hs_REFSEQ_10) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm) to normalize the microarrays, and MAS5 to get present/absent calls. LIMMA was used to identify probe sets whose expression levels were significantly changed after 4, 8, or 12 hours of hypoxia relative to the normoxic signal. The MAS5 present/absent calls were assigned values of absent=0, marginal=0.5, or present=1. For each probe set, the sum of triplicate samples was partitioned into “present” if sum≥2, and “absent” if sum<2.
 
Submission date Oct 09, 2009
Last update date Oct 09, 2009
Contact name Xiaobo Xia
E-mail(s) Xiaobo_Xia@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Pediatric Oncology
Lab Dr. Andrew Kung
Street address 44 Binney St, Mayer 649
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL9419
Series (2)
GSE18494 Expression profiling of hypoxic HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells: time course
GSE18505 HepG2 hepatoma and U87 glioma cells: transcriptomic and genomic analyses

Data table header descriptions
ID_REF
VALUE normalized signal intensity
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
NM_000014_at 13.63923904 P
NM_000015_at 2.087296393 A
NM_000016_at 8.78549162 P
NM_000017_at 6.676615381 P
NM_000018_at 9.469287291 P
NM_000019_at 10.64216101 P
NM_000020_at 2.243910108 A
NM_000021_at 6.681251781 P
NM_000022_at 2.636296371 P
NM_000023_at 2.423539289 A
NM_000024_at 1.93864238 A
NM_000025_at 2.340109754 A
NM_000026_at 10.29592601 P
NM_000027_at 4.805372247 P
NM_000028_at 7.783693227 P
NM_000029_at 12.90693218 P
NM_000030_at 6.966419744 P
NM_000031_at 5.716466609 P
NM_000032_at 2.07621138 A
NM_000033_at 7.981783434 P

Total number of rows: 22759

Table truncated, full table size 607 Kbytes.




Supplementary file Size Download File type/resource
GSM460679.CEL.gz 8.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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