|
| Status |
Public on Sep 12, 2013 |
| Title |
shCypB1 |
| Sample type |
RNA |
| |
|
| Source name |
human glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U251
transduction: stably expressing shRNA against cyclophilin B
|
| Treatment protocol |
U251 GBM cells were transduced with the lentiviral shRNA (shCON or shCypB) for 5 days before total RNA extraction. The pLKO1.5 vectors (shCON encoding non-target control sequence and shCypB to target CypB gene) were used to generate lentiviral particles.
|
| Growth protocol |
U251 GBM cells were grown in DMEM with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy RNA isolation kit from Qiagen
|
| Label |
biotin
|
| Label protocol |
standard as recommended by illumina
|
| |
|
| Hybridization protocol |
standard as recommended by illumina
|
| Scan protocol |
standard as recommended by illumina
|
| Description |
U251 shRNA against CypB, biological replicate A
|
| Data processing |
Fastlo [1] normalization was used to preprocess the data. In the quality control step, the Principal Components Analysis (PCA) graph and the hierarchical clustering plot (based on Pearson’s dissimilarity) showed a plate effect, which was removed later using Partek’s batch removal tool[2]. 1. J. E. Eckel, C. Gennings, T. M. Therneau, L. D. Burgoon, D. R. Boverhof, and T. R. Zacharewski. Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics (2005) 21(7): 1078-1083. 2. Removing Batch Effects in Partek. Partek® software On-line Help, version 6.5, build 6.10.0915. Copyright © 2010 Partek Inc., St. Louis, MO, USA.
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
Sep 12, 2013 |
| Contact name |
Richard J Bram |
| E-mail(s) |
richard.bram@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Pediatric and Adolescent Medicine
|
| Street address |
200 First Street SW
|
| City |
ROCHESTER |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE50756 |
Cyclophilin B supports the survuval of glioblastoma multiforme cells |
|
