|
| Status |
Public on Mar 25, 2012 |
| Title |
BLCL_2.1 |
| Sample type |
RNA |
| |
|
| Source name |
EBV-transformed lymphoblastoid cell line from subject 2.1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EBV-transformed lymphoblastoid cells
origin: lymphoid
subject: 2.1
|
| Treatment protocol |
Not treated.
|
| Growth protocol |
B-LCLs and B cells were grown in RPMI 1640 medium supplemented with 25mM HEPES, 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. HEK293 and HeLa cells were grown in DMEM medium supplemented with 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. Exponential growth under normal conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the miRNeasy mini kit, including on-column DNase I treatment (Qiagen), according to the manufacturer’s instructions. Total RNA was quantified using the NanoDrop 2000 (Thermo Scientific) and RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
100 ng of each RNA sample was labeled with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized to the Agilent Human microRNA Microarray Release 16.0 (G4872A-031181 Agilent Technologies) with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.
|
| Scan protocol |
Slides were scanned with a GenePix 4000B scanner (Molecular Devices) at a 5uM/pixel resolution .
|
| Data processing |
Features were extracted with the GenePix 6.1 software. Analyses were performed using BRB-ArrayTools Version 4.2.0 Stable Release developed by Dr. Richard Simon and the BRB-ArrayTools Development Team (http://en.bio-soft.net/chip/BRBArrayTools.html). The data were background-subtracted and quantile normalized. To estimate a single intensity measure for each miRNA, we calculated the mean of its different probes.
|
| |
|
| Submission date |
Jan 24, 2012 |
| Last update date |
Mar 25, 2012 |
| Contact name |
Diana Paola Granados |
| Organization name |
IRIC
|
| Department |
Medecine
|
| Lab |
Immunobiologie
|
| Street address |
C.P. 6128, succursale Centre-ville
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3C 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15159 |
| Series (1) |
| GSE35319 |
MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements |
|
