|
| Status |
Public on Apr 01, 2013 |
| Title |
B6-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow derived mast cells
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: C57BL/6J
genotype/variation: normal control
|
| Treatment protocol |
BMMCs were purified by negative selection with MicroBeads (Miltenyi Biotec) after 4 weeks in culture. The cells were further rested in cytokine free medium for 4h.
|
| Growth protocol |
Bone marrow derived mast cells (BMMCs) from AhR null, AhR_d and normal control mice were cultured in 30% WEHI-3-conditioned medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with RNeasy mini kits with DNase I treatment (Qiagen) in accordance with the prescribed protocol provided with the kit and stored at -80°C. The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to Illumina Sentrix® Murine Ref8_v2_R3 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol
|
| Scan protocol |
All signal intensity quantification was performed using an Illumina iScan scanner, using the standard Illumina scanning protocol.
|
| Description |
batch 3
|
| Data processing |
A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina GenomeStudio software with standard settings and no background correction. The expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed.
|
| |
|
| Submission date |
Feb 27, 2013 |
| Last update date |
Apr 01, 2013 |
| Contact name |
Alan E. Berger |
| E-mail(s) |
alanberger@alum.mit.edu
|
| Phone |
301-938-3565
|
| Organization name |
Johns Hopkins University
|
| Department |
School of Medicine
|
| Lab |
Division of Allergy and Clinical Immunology
|
| Street address |
5501 Hopkins Bayview Circle Room 3B.74C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE44715 |
Mast cell expression data from murine aryl hydrocarbon receptor (AhR) null, AhR_d and normal control mice |
|
