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Sample GSM774481 Query DataSets for GSM774481
Status Public on Nov 21, 2012
Title Typically Developing Control, Semitendinosus, Patient Replicate 6
Sample type RNA
 
Source name Semitendinosus Muscle, Control
Organism Homo sapiens
Characteristics subject: 28
disease: TD
muscle: ST
gender: M
age: 14.8
gmfcs: N/A
popliteal angle: N/A
Extracted molecule total RNA
Extraction protocol Rneasy Kit (Qaigen) extration of total RNA was performed
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2-5 ug total RNA
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45oC on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Data processing GeneSpring Software (Affymetrix, version 11.5) was used for primary analysis. Genes were denoted as present if they had a MAS5 present call on 10/40 chips. The concordance of 3 summarization algorithms were used: MAS5, RMA, and GC-RMA. Significantly altered genes were determined by a 2x2 ANOVA within GeneSpring on patient group (cerebral palsy or control patients) and muscle (gracilis or semitendinosus) with a False Discovery Rate set at 1%. This analysis was performed on each of the three summarization algorithms and the overlap of all 3 was used as the significantly different gene set. The RMA and GCRMA in log2 format values are linked to the Series record.
 
Submission date Aug 05, 2011
Last update date Nov 21, 2012
Contact name Lucas Robert Smith
E-mail(s) lrs001@ucsd.edu
Organization name University of California San Diego
Department Bioengineering
Lab Muscle Physiology Laboratory
Street address 3350 La Jolla Village Drive Mail Code 151
City San Diego
State/province CA
ZIP/Postal code 92161
Country USA
 
Platform ID GPL571
Series (1)
GSE31243 Transcriptional Alterations of Hamstring Muscle Contractures in Children with Cerebral Palsy

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 3057.2 P 0.000754
AFFX-BioB-M_at 4061.8 P 0.000044
AFFX-BioB-3_at 3331.3 P 0.00007
AFFX-BioC-5_at 7914.2 P 0.000052
AFFX-BioC-3_at 11533.6 P 0.000044
AFFX-BioDn-5_at 22207.2 P 0.000044
AFFX-BioDn-3_at 37875.8 P 0.00007
AFFX-CreX-5_at 105756.2 P 0.000052
AFFX-CreX-3_at 125528.1 P 0.000044
AFFX-DapX-5_at 67.6 A 0.41138
AFFX-DapX-M_at 69.7 A 0.760937
AFFX-DapX-3_at 20.8 A 0.973889
AFFX-LysX-5_at 70.9 A 0.41138
AFFX-LysX-M_at 76 A 0.631562
AFFX-LysX-3_at 148.2 P 0.013811
AFFX-PheX-5_at 37.4 A 0.724854
AFFX-PheX-M_at 5.3 A 0.998407
AFFX-PheX-3_at 87.9 A 0.631562
AFFX-ThrX-5_at 13.9 A 0.984817
AFFX-ThrX-M_at 12.8 A 0.834139

Total number of rows: 22277

Table truncated, full table size 605 Kbytes.




Supplementary file Size Download File type/resource
GSM774481.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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