|
| Status |
Public on Nov 12, 2013 |
| Title |
FreshBs_untreated_S_341_B |
| Sample type |
RNA |
| |
|
| Source name |
FreshBs_untreated
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: Peripheral blood mononuclear cells
cell subtype: native B cells
treated with: sham buffer for 24 h
|
| Treatment protocol |
B-cells and LCLs were incubated with either 2 µM activated simvastatin or a sham buffer for 24 hours in RPMI media supplemented with 500 U/ml penicillin/streptomycin, 10% FBS and 2 nmol/L GlutaMAX, and all cultures were maintained at 37°C with 5% CO2. The B-cells were statin or sham exposed at the time of isolation while LCLs were frozen, thawed and exposed as a single batch. Simvastatin, obtained as a gift from Merck, was activated.
|
| Growth protocol |
Peripheral blood mononuclear cells (PBMCs) were isolated from 10ml of blood using IsoPrep (Matrix Technologies) and transformed by EBV. Viable cells remaining after six weeks were considered to be LCLs. PBMCs were isolated from the remaining 50ml of blood using Lymphoprep (VWR), and B-lymphocytes were specifically isolated from PBMCs using the B-cell Negative Isolation kit (Invitrogen) according to the manufacturer's protocol. Aliquots of B-cells were incubated with FITC-conjugated CD19 fluorescent antibodies and the proportion of CD19 positive cells (B-cells only) was determined by FACS analysis (BD FACS Calibur) of 10,000 gated events. Only preparations with >90% B-lymphocyte purity were used for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from all samples and stored at -80°C.
|
| Label |
biotin
|
| Label protocol |
All RNAs were converted to biotin-labeled cRNA using the Illumina TotalPrep-96 RNA amplification kit (Applied Biosystems, Foster City, CA) in a single batch.
|
| |
|
| Hybridization protocol |
cRNA was randomized and hybridized in a single batch to Illumina HumanHT-12_V4 expression beadchips (Illumina, San Diego, CA) at Channing Laboratory (Division of Network Medicine, Brigham and Women's Hospital, Boston MA) according to the manufacturer’s protocols.
|
| Scan protocol |
Manufacturer standard.
|
| Description |
ST-01000679_S-001009656_5522887082_E
|
| Data processing |
R lumi package was used for analysis, log2 values were quantile normalized
|
| |
|
| Submission date |
Oct 18, 2013 |
| Last update date |
Nov 12, 2013 |
| Contact name |
Eugene L Bolotin |
| Organization name |
UC Riverside
|
| Department |
Cell Biology and Neuroscience
|
| Lab |
Frances Sladek Lab
|
| Street address |
900 university ave
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE51444 |
Statin induced changes in gene expression in EBV-transformed and native B-cells |
|
