|
| Status |
Public on May 08, 2015 |
| Title |
ALS without C9ORF72 mutation 22 |
| Sample type |
RNA |
| |
|
| Source name |
ALS without C9ORF72 mutation
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Patient49
patient group: ALS not due to mtC9ORF72
cell type: Cultured lymphoblastoid cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from approximately 5x10^6 lymphoblasotoid cells using the Qiagen RNeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylation of antisense RNA carried out according to Affymetrix protocol
|
| |
|
| Hybridization protocol |
6-10µg of cRNA molecules were heat fragmented and applied to the Human Exon 1.0ST GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
|
| Scan protocol |
Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols
|
| Description |
Lymphoblastoid cells derived from individual without mutated C9ORF72
|
| Data processing |
Data were normalised using puma package (PMID: 23379655). Puma quantifies uncertainty to improve estimation of transcript expression values. A custom cdf (HuexonSpecificGeneProbes.tsv) and annotation file (ranscripts-human-annotation.R.gz) were obtained through GATExplorer.
The 'transcripts-human-annotation.R.gz' annotation file (http://bioinfow.dep.usal.es/xgate/downloads_v57/transcripts-human-annotation.R.gz) was downloaded from http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=annotationfiles
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
May 08, 2015 |
| Contact name |
Paul Roy Heath |
| E-mail(s) |
p.heath@sheffield.ac.uk
|
| Phone |
+44 114 2222254
|
| Organization name |
University of Sheffield
|
| Department |
Academic Neurology Unit
|
| Lab |
Heath
|
| Street address |
SITraN, 385a Glossop Road
|
| City |
Sheffield |
| State/province |
S. Yorks |
| ZIP/Postal code |
S10 2HQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20149 |
| Series (2) |
| GSE68607 |
C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis [HuEx-1_0-st] |
| GSE68608 |
C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis |
|
