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Sample GSM892379 Query DataSets for GSM892379
Status Public on Sep 19, 2012
Title Biceps, control, cohort 20, subject 20U
Sample type RNA
 
Source name Biceps, control, cohort 20, subject 20U
Organism Homo sapiens
Characteristics subject: 20U
cohort: 20
tissue: Biceps
disease state: control
ecori/blni allele length: 39kb
age (y): 48
Sex: F
batch: Batch_5
Extracted molecule total RNA
Extraction protocol A portion of each biopsy sample (ranging between 50-200mg) was snap frozen in liquid nitrogen immediately after procurement and stored at -80°C for RNA extraction. Total RNA was isolated from frozen muscle tissues using TRIzol reagent (Invitrogen).
Label biotin
Label protocol Biotin-labeled target for the microarray experiment was prepared using 100 ng of total RNA and cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix). The sense cDNA was then fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix).
 
Hybridization protocol Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human Gene 1.0 ST array (Affymetrix) at 45°C for 16–20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix)
Scan protocol The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix).
Description Gene expression data from Biceps, control, cohort 20, subject 20U
Data processing Array data were preprocessed using RMA (apt-1.14.2 and HuGene-1_0-st-v1.r4.analysis-lib-files) and analyzed using the limma package (version 3.8.2, R version 2.11.1, and hugene10sttranscriptcluster.db_7.0.1). Note that arrays were scanned on several different dates (indicated by batch number in sample description), and when computing expression differences it is advisable to include a factor to correct for the batch effects, either directly of with a factor for cohort (as samples within each cohort were scanned on the same date).
 
Submission date Mar 09, 2012
Last update date Sep 19, 2012
Contact name Fedik Rahimov
E-mail(s) frahimov@enders.tch.harvard.edu
Phone 617-355-4042
Fax 617-730-0253
Organization name Boston Children's Hospital
Department Genetics
Lab Kunkel
Street address 3 Blackfan Circle, CLS 15030.4
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL6244
Series (1)
GSE36398 Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
7892501 2.24425
7892502 4.98887
7892503 2.82436
7892504 8.80833
7892505 3.22063
7892506 4.674
7892507 5.05578
7892508 5.28808
7892509 10.70124
7892510 3.86176
7892511 3.2882
7892512 6.72701
7892513 4.03318
7892514 8.26554
7892515 9.3754
7892516 2.83486
7892517 6.55961
7892518 3.09566
7892519 5.03536
7892520 9.21128

Total number of rows: 33297

Table truncated, full table size 518 Kbytes.




Supplementary file Size Download File type/resource
GSM892379_Sample_20UBIC.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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