|
| Status |
Public on Sep 22, 2009 |
| Title |
m2_Tnaive |
| Sample type |
RNA |
| |
|
| Source name |
Sorted CD4+ T cells, naïve
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6
Gender: male
Age: 15 weeks
Tissue: pooled spleen and lymph nodes
|
| Treatment protocol |
Sorted lymphocytes.
|
| Growth protocol |
Primary cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified with the RNEasy mini kit (Qiagen) with on-column DNAse treatment according to manufacturer's instructions. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto).
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturer’s protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE).
|
| |
|
| Hybridization protocol |
Equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol (Agilent).
|
| Scan protocol |
Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).
|
| Description |
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 1
|
| Data processing |
This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). This procedure was carried out using the Bioconductor package limma (http://www.bioconductor.org). No background subtraction was performed.
|
| |
|
| Submission date |
Nov 06, 2008 |
| Last update date |
Sep 22, 2009 |
| Contact name |
Mark Klinger |
| E-mail(s) |
mark.klinger@ucsf.edu
|
| Phone |
415-502-5432
|
| Organization name |
University of California, San Francisco
|
| Department |
Microbiology and Immunology
|
| Lab |
Nigel Killeen
|
| Street address |
513 Parnassus Avenue, Box0414
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94122 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE13502 |
Gene expression analysis of Ox40-cre/ROSA-YFP CD4+ T cell subsets |
|
