|
| Status |
Public on Oct 12, 2008 |
| Title |
Rag-IgH_232 |
| Sample type |
RNA |
| |
|
| Source name |
Pre-B cells from RAG-1-deficient mice with an IgH transgene
|
| Organism |
Mus musculus |
| Characteristics |
Purified whole cell RNA
|
| Biomaterial provider |
Generated from RAG-1-/-:IgH mice in our laboratory
|
| Treatment protocol |
RNA from purified bone marrow B cells
|
| Growth protocol |
RNA harvested immediately after purification of cells from bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNeasy technology following the manufacturer?s instructions.
|
| Label |
biotin
|
| Label protocol |
Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification One-Cycle Target labeling kit according to manufacturerís 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 GenechipÆ Operating Software (Version 1.2.0.037).
|
| Description |
Gene expression analysis was conducted using Mouse 430v2 GenechipÆ arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification One-Cycle Target labeling kit according to manufacturerís 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 GenechipÆ Operating Software (Version 1.2.0.037).
|
| Data processing |
The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1). 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, 2008 |
| 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 |
