|
| Status |
Public on Jan 05, 2016 |
| Title |
DM2_F_37_VL [gene-level] |
| Sample type |
RNA |
| |
|
| Source name |
Skeletal Muscle- vastus lateralis
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Myotonic Dystrophy Type 2
gender: F
age (yrs): 37
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the TriZol Reagent according to the manufacturer's suggestions (Invitrogen, Carlsbad, CA) and further purified using the RNeasy kit (Qiagen Inc., Valencia, CA). The quality and integrity of the RNA was then analyzed on an Agilent Bio- Analyzer (RNA 6000 Nano LabChip). Total cellular RNA samples with a RIN (RNA integrity number) >7 were used for further microarray studies
|
| Label |
biotin
|
| Label protocol |
RNA was processed for hybridization using Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay for preparation of single-stranded (ss) target DNA
|
| |
|
| Hybridization protocol |
Sample hybridization, washing and scanning was performed according to manufacturer’s recommendations.
|
| Scan protocol |
Scanning was performed using the Affymetrix GeneChip Scanner according to manufacturer’s recommendations. Images were processed using GCOS manager v1.4.0.036 and GCDO v5.0.9.
|
| Description |
DM2_KL_064_EA_HUEX1ST_20051215_TN.CEL
|
| Data processing |
CEL files were analyzed using the Partek Genomics Suite (Partek Inc., St. Louise, MO), employing the workflow for exon arrays, and aligned to genome Build hg18. Only the core set of probes (as defined by Affymetrix) were included. Intensities were quartile normalized with RMA background correction but without GC correction.
probe_group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Jul 12, 2013 |
| Last update date |
Jan 05, 2016 |
| Contact name |
Mario Sirito |
| E-mail(s) |
msirito@mdanderson.org
|
| Organization name |
M. D. Anderson Cancer Center
|
| Department |
Cancer Genetics
|
| Street address |
1515 Holcombe blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE48828 |
Expression and Splicing Analysis of Myotonic Dystrophy and Other Dystrophic Muscle |
|
| Relations |
| Alternative to |
GSM1185355 (exon-level analysis) |
