|
| Status |
Public on May 05, 2016 |
| Title |
CLBL1 |
| Sample type |
RNA |
| |
|
| Source name |
CLBL1 cell line
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: CLBL1
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Cells were cultured in RPMI media supplemented with 20% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol method and DNase treated. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
A 2 µg aliquot of total RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences).
|
| |
|
| Hybridization protocol |
Then, 15 µg of labeled cRNA was fragmented following the manufacturer instructions. Labeled cRNA targets were hybridized to Affymetrix GeneChip® Canine Genome 2.0 array for 16 hours at 45 °C rotating at 60 rpm.
|
| Scan protocol |
Arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000 (Affymetrix). For gene expression analysis, arrays were normalized.
|
| Description |
Canine B cell lymphoma cell line
|
| Data processing |
For clustering, we downloaded supplementary microarray data (GSE43664) from GEO, then merged the microarray data for CLBL1 and processed the combined data using the robust multiarray averaging (RMA) method in version 3.1.2 of the R statistical programming environment. We then applied the median polish algorithm to the subset of 1180 canine probe sets found to separate two subtypes of canine B-cell lymphoma (9). Samples were clustered using centroid linkage and a distance metric based on un-centered correlation. To confirm the cluster assignment, we computed distance from CLBL1 to the centers of both the GCB and ABC clusters using three methods: Euclidean, Pearson correlation, and un-centered correlation.
|
| |
|
| Submission date |
May 04, 2016 |
| Last update date |
May 05, 2016 |
| Contact name |
Bonnie Kate Harrington |
| E-mail(s) |
harrington.120@osu.edu
|
| Organization name |
Ohio State University
|
| Street address |
410 W 12 Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL3738 |
| Series (1) |
| GSE81110 |
Classifying the Canine B-cell Lymphoma Cell line CLBL1 |
|
