|
| Status |
Public on Aug 30, 2012 |
| Title |
GEP_MCL25 |
| Sample type |
RNA |
| |
|
| Source name |
Mantle cell lymphoma from lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
tumour: MCL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
|
| Label |
Biotin
|
| Label protocol |
Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
|
| Scan protocol |
GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
|
| Description |
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Data processing |
Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
|
| |
|
| Submission date |
Jan 30, 2012 |
| Last update date |
Aug 30, 2012 |
| Contact name |
Alan J Watkins |
| E-mail(s) |
a.j.watkins@doctors.org.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Addenbrooke's Hospital
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE21554 |
An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Main Study) |
| GSE35426 |
An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Affymetrix HG-U133plus2 gene expression microarray) |
|
