|
| Status |
Public on Jul 24, 2020 |
| Title |
CD4+ naïve cells from WT mice, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
CD4+ naïve cells from WT mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4+ naïve cells
genotype/variation: WT
strain: C57BL/6J
experimental condition: ex vivo isolated
|
| Treatment protocol |
T naïve cells were sorted as CD4+ or CD8+, CD62L+, CD44- and CD25- cells, while TEM cells were sorted as CD4+ or CD8+, CD62L-, CD44+ and CD25- cells
|
| Growth protocol |
CD4+ T naïve and TEM cells were sorted at FACSAria (BD Biosciences) from pooled cell suspensions of spleen, inguinal, axillary, brachial, cervical and mesenteric lymph nodes collected from C57BL/6J and P2rx7-/- mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneasy (Qiagen, Hilden, Germany) accordingly to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using GeneChip™ 3' IVT PLUS Reagent Kit (Thermo Fisher Scientific Santa Clara, California, United States) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized on MG-430 PM array strips. GeneChip strip was washed and stained in the Affymetrix GeneAtlas Platform according to the manufacturer's instructions
|
| Scan protocol |
GeneChip strip images were acquired using the GeneAtlas Imaging Station and the GeneAtlas Instrument Control (GAIC) software according to the standard Affymetrix protocol
|
| Description |
Gene expression profile of CD4+ naïve cells from WT mice
|
| Data processing |
RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF HTMG430PM_Mm_ENTREZG_22.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization. Batch correction using the ComBat function of the sva package was applied to remove some batch effect affecting replicate 2 samples of TEM cells from WT and P2rx7-/- mice (batch 1), as compared to all other samples (batch 2).
|
| |
|
| Submission date |
Aug 06, 2018 |
| Last update date |
Jul 24, 2020 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL25426 |
| Series (1) |
| GSE118146 |
Expression data of ex vivo purified CD4+ cells from WT and P2rx7-/- mice |
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