|
| Status |
Public on Sep 26, 2013 |
| Title |
Lymph_node_biopsy_DLBCL_sample_18 |
| Sample type |
RNA |
| |
|
| Source name |
Lymph node biopsy, diffuse large B-cell lymphoma (DLBCL)
|
| Organism |
Canis lupus familiaris |
| Characteristics |
case id: 123454
disease state: DLBCL
current medications: None
previous chemo (yes or no): Yes
if yes chemo protocol: CHOP(started 24Mar08)CCNU/L-Aspar/Pred (started 28Apr08)
time since last treatment (days): 76
age (yrs): 10.8
Sex: M/N
breed: Siberian Husky
rna integrity number: 9.1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed in two balanced random batches by polytron homogenisation of tissue in Trizol (cat. 15596-026, Invitrogen) followed by phenol chloroform extraction. RNAs were quantitated and qualified using Nanodrop ND8000 (Thermo Scientific) and 2100 Bioanalyser (Agilent). Prior to cDNA probe generation RNAs were subjected to sample clean up and DNAse I treatment using RNEasy Micro (Qiagen) before repeat quantitation and qualification.
|
| Label |
biotin
|
| Label protocol |
50ng RNA from each sample were used to generate complementary DNA strands using Ovation RNA Amplification System V2 (cat. 3100-12, Nugen) and 3.75ug of each cDNA were fragmented and biotin labelled using Encore™ Biotin Module (cat. 4200-12, Nugen).
|
| |
|
| Hybridization protocol |
Probe quality and fragmentation were confirmed using Bioanalyser 2100 prior to microarray hybridisation. Fragmented and labelled probes were hybridised for 18 hours onto Affymetrix GeneChip Canine Genome 2.0 Array (cat. 900725, Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (cat. 900720, Affymetrix).
|
| Scan protocol |
Microarrays were scanned using Genechip Scanner 3000 7G.
|
| Data processing |
The data in the matrix table were generated in the Affymetrix Expression Console and normalised using RMA method in Partek GS 6.5. Microarray data were generated from all the 35 canine samples (25 DLBCL and 10 healthy). However, data from 2 canine DLBCL samples (EU121 Sample 07 1 26-10-09.CEL and EU121 Sample 17 1 27-10-09.CEL) did not meet our required quality and were removed from further analysis. Only data from 33 (23 DLBCL and 10 healthy) samples were used for analysis.
|
| |
|
| Submission date |
Jul 22, 2011 |
| Last update date |
Sep 26, 2013 |
| Contact name |
Manikhandan A V Mudaliar |
| E-mail(s) |
innovatebio@gmail.com
|
| Organization name |
University of Glasgow
|
| Department |
College of Medical, Veterinary and Life Sciences
|
| Lab |
Institute of Infection, Immunity and Inflammation
|
| Street address |
Room B528, Sir Graeme Davies Building, 120 University Place
|
| City |
Glasgow |
| State/province |
Scotland |
| ZIP/Postal code |
G12 8TA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3738 |
| Series (1) |
| GSE30881 |
Comparative Transcriptional Analysis of Canine and Human Diffuse Large B cell Lymphoma (DLBCL). Molecular Signatures of NF-κB Pathway Activation and Sub-Classification of Canine DLBCL. |
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