|
| Status |
Public on Oct 12, 2008 |
| Title |
R2K Bcl.2 |
| Sample type |
RNA |
| |
|
| Source name |
RAG-2-deficient v-abl-transformed pre-B cell
|
| Organism |
Mus musculus |
| Characteristics |
G1-phase pre-B cells
|
| Biomaterial provider |
Generated from RAG-2-/- mice in our laboratory
|
| Treatment protocol |
3um STI571 for 48 hours
|
| Growth protocol |
Treated at 1 million cells per ml in DMEM 10% FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNeasy technology following the manufacturer¹s instructions.
|
| Label |
biotin
|
| Label protocol |
Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
|
| Scan protocol |
Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Description |
Gene expression analysis was conducted using Mouse 430v2 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Data processing |
The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 6.0). This system performs data pre-processing and error modeling as described in Weng (2006). Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.
|
| |
|
| Submission date |
Aug 13, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE9024 |
Gene activation by Rag-mediated DNA double strand breaks |
|
| Relations |
| Reanalyzed by |
GSE119085 |
