|
| Status |
Public on Aug 30, 2012 |
| Title |
Custom_Oligo_2Kb_aCGH_SMZL5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Spleen, SMZL patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: spleen
disease: splenic marginal zone lymphoma
|
| Growth protocol |
Spleens were fresh frozen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard phenol-chloroform isoamyl alcohol extraction.
|
| Label |
Cy5
|
| Label protocol |
BioPrime aCGH labelling system (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Pooled PBMCs, 10 normal subjects
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard phenol-chloroform isoamyl alcohol extraction.
|
| Label |
Cy3
|
| Label protocol |
BioPrime aCGH labelling system (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Arrays were performed as per Agilent manufacturer's instructions. Briefly, array blocking was performed using Agilent 10X blocking agent, and labelled DNA suspended in Agilent 2x HiRPM Hybridization buffer. Samples were hybridized for 24hrs at 65 degrees. Washing was performed with 5 minutes in Agilent oligo aCGH wash buffer 1 at RT, and 1 minute in buffer 2 at 37 degrees.
|
| Scan protocol |
Scanning was perfomed in an Agilent High Resolution C scanner at 3 microns resolution.
|
| Description |
C5
|
| Data processing |
Data was analyzed using the Agilent Feature Extraction Software (v10.5) and visualized in Genomic Workbench Standard Edition (v5.0.14). Data was normalized using Lowess.
|
| |
|
| Submission date |
Jan 23, 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 |
GPL10383 |
| Series (2) |
| GSE21554 |
An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Main Study) |
| GSE35425 |
An integrated genomic and expression analysis of 7q deletion in SMZL (Oligo aCGH) |
|
