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Status |
Public on Dec 08, 2021 |
Title |
AT4 naive CD8 |
Sample type |
RNA |
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Source name |
Mouse spleen CD8 T-cells_Navie CD8
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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: Navie CD8
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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).
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
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Label |
biotin
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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
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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
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Scan protocol |
Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.
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Description |
Navie CD8 replicate 4
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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.
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Submission date |
Aug 02, 2017 |
Last update date |
Dec 08, 2021 |
Contact name |
Martina Seiffert |
Organization name |
German Cancer Research Center
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Department |
Department of Molecular Genetics
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Street address |
Im Neuenheimer Feld 280
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City |
Heidelberg |
ZIP/Postal code |
69120 |
Country |
Germany |
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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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