|
| Status |
Public on Oct 16, 2014 |
| Title |
WT, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mature CD4SP thymocytes, wild-type
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mature CD4SP thymocytes
genotype: wild-type
background strain: C57BL/6
|
| Treatment protocol |
NA
|
| Growth protocol |
Hematopoietic chimeras were generated by reconstituting lethally irradiated CD45.1+ hosts with a mix of CD45.1+CD45.2+ Rag1-GFP WT and CD45.2+ Rag1-GFP blt/blt bone marrow. Cells were isolated from the thymus by mechanical disaggregation through a 40μm nylon sieve, and CD4SP thymocytes were enriched by MACS depletion with anti-CD8 microbeads (Miltenyi Biotech) prior to sorting. WT and bloto mature CD4SP thymocytes (GFPhi CD4+ CD8− CD62Lhi CD69lo) were sorted on a FACSAria with ≥98% purity. Dead cells were excluded with DAPI.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Micro Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized and amplified using the Ovation Pico WTA System V2 (NuGEN, San Carlos, CA). The resulting libraries were fragmented and labeled using the Encore Biotin Module (NuGEN).
|
| |
|
| Hybridization protocol |
Labeled libraries were hybridized to Affymetrix Mouse 1.0 ST arrays according to Affymetrix's GeneChip Expression Analysis Technical Manual 702232 Rev. 3. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G System.
|
| Description |
Gene expression data from WT mature CD4SP thymocytes
|
| Data processing |
Affymetrix CEL files containing raw, probe-level signal intensities were analyzed in Bioconductor using the affy R package, with RMA normalization and probeset definitions from Brainarray custom CDF (mogene10st_Mm_ENTREZG_17.1.0).
|
| |
|
| Submission date |
Jun 06, 2014 |
| Last update date |
Oct 16, 2014 |
| Contact name |
Brenda Yuyuan Han |
| Organization name |
Institute of Molecular and Cell Biology, A*STAR
|
| Street address |
61 Biopolis Drive, Proteos
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17777 |
| Series (2) |
| GSE58288 |
Gene expression profiling of mature CD4 SP thymocytes from a mouse strain with an ENU-induced mutation in Zfp335 |
| GSE58293 |
Zinc finger protein Zfp335 is required for formation of the naïve T cell compartment |
|
