|
| Status |
Public on Mar 22, 2012 |
| Title |
BEAS-2B_Contrl_Clone_rep_1 |
| Sample type |
RNA |
| |
|
| Source name |
agar-derived clone_not treated_paired with As and Ni clones
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: BEAS-2B
background cell type: immortalized human bronchial epithelial cell
cell type: agar-derived control clone
|
| Treatment protocol |
Cells were treated with an aqueous filter-sterlized solution of metals at the concentrations and days indicated prior to seeding in soft agar; metal was removed before seeding in soft agar and for the remainder of the experiment.
|
| Growth protocol |
cell were grown under standard laboratory conditions in DMEM supplemented with 10% FBS and 1% PenStrep; a single cell suspension of 5,000 cells per 9.6 square cm was seeded in soft agar at a concentration of 0.35%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol and purified using RNeasy Plus Micro Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
The cDNA probes were synthesized using the WT Expression Kit for Affymetrix Whole Transcript Expression Arrays (Ambion), fragmented, and labeled using Affymetrix Whole Transcript Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
cRNA generated by the labeling procedure was hybridized for 16 hr to the Affymetrix array according to the manufacturer's manual. Genechips were processed using protocol FS450_0007 for Genechip® fluidics station 450.
|
| Scan protocol |
Affymetrix GeneArray scanner 7G
|
| Description |
Ctrl-1
|
| Data processing |
Feature intensity was extracted by GeneChip Operating System as CEL files; data from cel files were batch normalized in R using the COMBAT package. The probe-level analysis of the batch-normalized data was done by the RMA-16 algorithm using GeneSpring GX11.5 program.
|
| |
|
| Submission date |
Mar 21, 2012 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Hailey A. Clancy |
| E-mail(s) |
[email protected]
|
| Phone |
(845) 731-3592
|
| Organization name |
New York University
|
| Department |
Environmental Medicine
|
| Lab |
Dr. Max Costa
|
| Street address |
57 Old Forge Road
|
| City |
Tuxedo |
| State/province |
NY |
| ZIP/Postal code |
10987 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE36684 |
Exposure of an immortalized human bronchial epithelial cell line, BEAS-2B, to one of four metals (arsenic, chromium, nickel or vanadium) to determine the early changes that lead to cell transformation |
|
| Relations |
| Reanalyzed by |
GSE86357 |
