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Status |
Public on Sep 12, 2013 |
Title |
shCON1 |
Sample type |
RNA |
|
|
Source name |
human glioblastoma cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: U251 transduction: stably expressing non-target control shRNA
|
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-Control, 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.
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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 |
|