|
| Status |
Public on Dec 08, 2021 |
| Title |
AT1 PD-1 int CD8 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse spleen CD8 T-cells_PD-1int
|
| Organism |
Mus musculus |
| Characteristics |
strain: C56BL/6
gender: female
transplanted with: murine CLL cells from Eµ-TCL1 mice
timepoint: 6 weeks of transplantation
cell type: spleen CD8 T-cells
cell subtype: PD-1int
|
| Growth protocol |
C57BL/6 mice transplanted with murine CLL cells and after 6 weeks total RNA was isolated from splenic CD8+ T-cell (Lin- TCRb+ CD8+) subsets that were sorted by flow cytometry from leukemic mice (Naïve: CD127hi CD44low, Memory: CD127hi CD44hi, PD-1int effector: CD127low CD44int-hi PD-1int, and PD-1hi effector: CD127low CD44int-hi PD-1hi).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled ss-cDNA samples for hybridization on GeneChip™ Mouse Gene 2.0 ST Arrays (Affymetrix) were prepared according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Pico Reagent Kit guide
|
| |
|
| Hybridization protocol |
20 μg of cRNA was then converted to sensestrand DNA (ss-cDNA). After fragmentation and terminal labeling, 5,5 ug of biotinylated ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays
|
| Scan protocol |
Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.
|
| Description |
PD-1int replicate 1
|
| Data processing |
Samples were processed with Affymetrix Power Tools using 'Robust Microarray Analysis' approach for the normalization. Log2-transformed transcript-level gene expression was calculated for ‘meta’ probe sets. Quality control of the samples was carried out by examining average raw intensity signal (pm_mean) or mean absolute deviation of the residuals (all_probeset_mad_residual_mean). 'Detected above background' measure was used to filter ‘meta’ probe sets if less than 50% of probe sets were called as ‘detected’ (P value <0.05) within less than 50% of the samples in each experimental group.
|
| |
|
| Submission date |
Aug 02, 2017 |
| Last update date |
Dec 08, 2021 |
| Contact name |
Martina Seiffert |
| Organization name |
German Cancer Research Center
|
| Department |
Department of Molecular Genetics
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16570 |
| Series (2) |
| GSE102149 |
Gene expression profiling of CD8+ T-cell subsets from TCL1-AT mice |
| GSE102602 |
Interleukin-10 receptor signaling promotes the maintenance of a PD-1int TCF-1+ CD8+ T cell population that sustains anti-tumor immunity |
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