|
| Status |
Public on May 26, 2011 |
| Title |
NC_DM2_HuEx |
| Sample type |
RNA |
| |
|
| Source name |
CDM1 primary muscle cells culture 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CDM1
|
| Growth protocol |
Skeletal muscle cell cultures derived from control and age-matched CDM1 fetus (36 weeks) were differentiated into myotubes for 10 days in D-MEM (Invitrogen) + 5µg/ml gentamycin + 10μg/ml insulin and 100μg/ml of transferrin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol protocol
|
| Label |
biotin
|
| Label protocol |
Samples were labeled according to GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix P/N 701880 Rev.2
|
| |
|
| Hybridization protocol |
5 micrograms of biotinylated cDNA were hybridized on GeneChip® Human Exon 1.0 ST array at 45°C for 16 hours
|
| Scan protocol |
The chips were scanned with the GeneChip® Scanner 3000 7G
|
| Description |
Primary culture of skeletal muscle cells of a CDM1 fetus, differentiation of 10 days
|
| Data processing |
Raw data (.CEL Intensity files) were generated using the Affymetrix GeneChip® Operating Software (GCOS) version 1.4. We then used Xray version 2.5 (BIOTIQUE Systems) to analyze the data on the core probe-sets at the exon level. The input files were normalized with quantile method. We applied the GC background correction and the expression score for each probe-set was derived via application of median-polish (ExonRMA). We filtered out probes with GC count less than 6 and greater than 17 and non-expressed probes using the DABG Filter Non Expressed Probes option. Nested Analysis of Variance was used to identify genes with alternative splicing.
|
| |
|
| Submission date |
May 12, 2010 |
| Last update date |
May 27, 2011 |
| Contact name |
Doulaye Dembele |
| E-mail(s) |
doulaye@igbmc.fr
|
| Phone |
+33 3 88 65 35 28
|
| Organization name |
IGBMC
|
| Department |
Biopuces
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67400 |
| Country |
France |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE21795 |
Misregulation of alternative splicing of BIN1 leads to T-tubule alterations and muscle weakness in myotonic dystrophy |
|
