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Sample GSM637907 Query DataSets for GSM637907
Status Public on Jan 13, 2011
Title inVitro6-Normox_NAg6P
Sample type RNA
 
Source name 9L glioma cells
Organism Rattus norvegicus
Characteristics strain: Fisher
cell type: 9L glioma cells
condition: Cells exposed to normoxia
Treatment protocol For in vivo samples: LCM was applied to EF5-positive and negative areas. For in vitro samples: To initiate the experiment, cells were either incubated at ~20% O2 (“Normoxia”) or 0.2% O2 (“Hypoxia”) for 6h or 16h. Cells were subsequently washed with HBSS (Invitrogen), detached with 0.25% trypsin-EDTA and resuspended in RNA lysis solution (Ambion) at a concentration of 50,000cells/100μl lysis solution.
Growth protocol Six week old male Fischer 344 rats (F344/Ncr, NCI-Frederick, MD) were inoculated via subcutaneous injection on the hind flank with 9L cells (106) to generate passage ‘zero’ tumors (p0). The tumor was excised, cut into 1-2mm3 pieces and used to generate subsequent passages. The epigastric tumors were initiated by tying p5 or p6 tumor pieces onto the epigastric artery-vein pair. 9L gliosarcoma cells were grown in MEM media with 12% newborn calf serum with twice-weekly transfer.
Extracted molecule total RNA
Extraction protocol The RNAqueous-micro kit from Ambion which includes an application for LCM-generated tissue was used to isolate total RNA. A DNase I treatment was performed according to the manufacturer’s protocol. An additional centrifugation step (14,000rpm for 1.5 min) and subsequent supernatant removal were performed to ascertain that all resin had been eliminated. Total RNA was linearly amplified using the NuGEN Ovation WT-Pico kit. Briefly, total RNA (2ng/sample) was reverse transcribed to generate cDNA that incorporated an RNA primer binding sequence. After second-strand synthesis, cDNA templates were amplified by ribo-SPIA. T
Label Biotin
Label protocol The resulting amplified cDNA was fragmented, biotinylated and hybridized to Rat Gene 1.0ST Arrays (Affymetrix).
 
Hybridization protocol Microarrays were stained with streptavadin-phycoerythrin and incubated with biotinylated anti-streptavadin to enhance fluorescence signal detection. Comparison of signal intensity yielded relative gene expression under hypoxia/normoxia.
Scan protocol standard Affymetrix scan protocol
Data processing Affymetrix .cel files were imported into Partek Genomics Suite (v6.5b, Partek Inc., St. Louis, MO). Robust Multichip Average (RMA) normalization was applied.
 
Submission date Dec 09, 2010
Last update date Jan 13, 2011
Contact name Constantinos Koumenis
E-mail(s) koumenis@xrt.upenn.edu
Organization name University of Pennsylvania
Department Radiation Oncology
Street address 3620 Hamilton Walk
City Philadelphia
State/province PA
ZIP/Postal code 19146
Country USA
 
Platform ID GPL6247
Series (1)
GSE25980 In vitro and in vivo analysis of hypoxic gene expression in rat gliomas

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
10778384 7.71331
10739986 7.66415
10769693 9.64237
10904578 3.39422
10908391 8.37841
10860806 3.23954
10860809 3.23954
10860812 3.23954
10890545 9.98441
10791358 3.95046
10909583 4.51429
10860815 3.63875
10905183 3.37629
10725748 3.64274
10771406 5.19702
10702293 7.02259
10853292 8.24772
10911014 8.14095
10742507 10.4733
10858275 7.82878

Total number of rows: 27363

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM637907.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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