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Sample GSM236921 Query DataSets for GSM236921
Status Public on Oct 09, 2008
Title TA side population 5Tsp
Sample type RNA
 
Source name Side population cells of TA
Organism Mus musculus
Characteristics C57BL/10ScSnJ mice were used to have SP cells of TA muscle
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA).
Label Biotin
Label protocol RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).
 
Hybridization protocol The GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).
Scan protocol Agilent model G2500A GeneArray scanner used.
Description SP cell preparations were washed, pelleted and resuspended in 20µl of PBS and stored at –80oC until processing for microarray analysis using manufacturers instructions and previously described methods from our laboratory . Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA). The purity, concentration and integrity of RNA was determined using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).
Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays. Raw intensities for each probe set were stored in electronic formats by expression summaries calculated using Microarray Suite version 5.0 (MAS5) algorithms.
Data processing MAS5 normalized data
 
Submission date Oct 11, 2007
Last update date Aug 28, 2018
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)
GSE9294 EOM and TA Sp cell comparison
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_Ref
VALUE Signal value
ABS_call Present, Absent, Marginal calls of the transcript
DETECTION P-VALUE MAS5 algorithm p-value for the transcript

Data table
ID_Ref VALUE ABS_call DETECTION P-VALUE
AFFX-BioB-5_at 759.4 P 0.00011
AFFX-BioB-M_at 1056.6 P 0.000052
AFFX-BioB-3_at 899.2 P 0.000052
AFFX-BioC-5_at 2174.1 P 0.000044
AFFX-BioC-3_at 1867.2 P 0.000052
AFFX-BioDn-5_at 5036 P 0.000044
AFFX-BioDn-3_at 9289.2 P 0.000044
AFFX-CreX-5_at 36674.3 P 0.000052
AFFX-CreX-3_at 39974.2 P 0.000044
AFFX-DapX-5_at 39.7 A 0.108959
AFFX-DapX-M_at 252.1 P 0.009337
AFFX-DapX-3_at 2765.1 P 0.000044
AFFX-LysX-5_at 24.3 A 0.238986
AFFX-LysX-M_at 100.2 P 0.046482
AFFX-LysX-3_at 946.4 P 0.000044
AFFX-PheX-5_at 1.7 A 0.999555
AFFX-PheX-M_at 84.4 P 0.042962
AFFX-PheX-3_at 618.7 P 0.000044
AFFX-ThrX-5_at 8.5 A 0.897835
AFFX-ThrX-M_at 25.1 A 0.368438

Total number of rows: 45101

Table truncated, full table size 1198 Kbytes.




Supplementary file Size Download File type/resource
GSM236921.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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