|
| Status |
Public on Sep 19, 2012 |
| Title |
Deltoid, FSHD, cohort 21, subject 21B |
| Sample type |
RNA |
| |
|
| Source name |
Deltoid, FSHD, cohort 21, subject 21B
|
| Organism |
Homo sapiens |
| Characteristics |
subject: 21B
cohort: 21
tissue: Deltoid
disease state: FSHD
ecori/blni allele length: 26kb
age (y): 59
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 Deltoid, FSHD, cohort 21, subject 21B
|
| 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 |
|
