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Sample GSM239148 Query DataSets for GSM239148
Status Public on Oct 10, 2009
Title Hypoxia-3
Sample type RNA
 
Source name Mouse quadriceps(QF) muscle
Organism Mus musculus
Characteristics Adult male C57Bl/10 mouse
Treatment protocol Adult male C57Bl/10 mice were used in experiments. At the beginning of the experiment mice were divided into two groups, control (room condition) and hypoxic (hypoxic condition), over a period of 2 weeks. The hypoxic group was gradually exposed to lower levels of hypoxia in an especially designed and hermetically closed hypoxic chamber. A Pegas 4000 MF(Columbus Instruments) gas blending system was used. The oxygen level was gradually decreased from 21% to 8% over one week and animals were kept at 8% oxygen for another 7 days.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from each QF muscle by Tri-Reagent (Ambion, Austin, TX) as described by manufacturer. Isolated total RNA were cleaned up by RNeasy mini kit (Qiagen, Valencia, CA) as described by manufacturer.
Label Biotin labeled
Label protocol Please see GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA) protocol.
 
Hybridization protocol Please see GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA) protocol.
Scan protocol Agilent model G2500A GeneArray scanner used.
Description The purity and concentration of total RNA were determined by measurement of absorbance at 260 and 280nm using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). To satisfy our purity criteria, we discarded all RNA samples that did not have a 260/280 ratio between 1.8 and 2.1. To satisfy our criteria for integrity, we required that all RNA used in our experiments have single peaks for the 18S and 28S bands as determined by the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).
Data processing MAS5 normalized data
 
Submission date Oct 22, 2007
Last update date Aug 14, 2011
Contact name Murat T Budak
E-mail(s) mtbudak@mail.med.upenn.edu
Phone 215-8989726
Organization name University of Pennsylvania
Department
Lab Rubinstein and Khurana Labs
Street address
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL1261
Series (1)
GSE9400 Hypoxic gene regulation on mice Quadriceps muscle

Data table header descriptions
ID_Ref
VALUE signal' a measure of the abundance of a transcript
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_Ref VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 755.5 P 0.000446
AFFX-BioB-M_at 1008.6 P 0.00007
AFFX-BioB-3_at 681.6 P 0.000857
AFFX-BioC-5_at 2467 P 0.00006
AFFX-BioC-3_at 2743.1 P 0.000044
AFFX-BioDn-5_at 5020.8 P 0.000044
AFFX-BioDn-3_at 11108.3 P 0.00006
AFFX-CreX-5_at 24771.2 P 0.000052
AFFX-CreX-3_at 27101.3 P 0.000044
AFFX-DapX-5_at 4412.9 P 0.000052
AFFX-DapX-M_at 7409.9 P 0.00007
AFFX-DapX-3_at 8762.4 P 0.000052
AFFX-LysX-5_at 561.9 P 0.00006
AFFX-LysX-M_at 790.8 P 0.000225
AFFX-LysX-3_at 1581.3 P 0.000052
AFFX-PheX-5_at 719 P 0.000052
AFFX-PheX-M_at 1230.8 P 0.000147
AFFX-PheX-3_at 976.3 P 0.000044
AFFX-ThrX-5_at 951.5 P 0.00011
AFFX-ThrX-M_at 1165.6 P 0.000044

Total number of rows: 45101

Table truncated, full table size 1220 Kbytes.




Supplementary file Size Download File type/resource
GSM239148.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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