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| Status |
Public on Feb 26, 2019 |
| Title |
iNKT cells RNA-Seq (WT vs SFR KO) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
RNA transcriptome difference between WT and SFR KO iNKT cells
To understand how SLAM family receptors (SFRs) contribute to iNKT cell development, a mouse lacking all SFRs in addition to the ligand of 2B4, CD48, was generated, and the transcriptional profiles of thymic iNKT cells from wild-type and SFR KO mice were compared, using RNA sequencing.
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| Overall design |
Examine RNA expression in WT and SFR KO iNKT cells
Thymocytes were isolated from WT and SFR KO mice, and iNKT cells were enriched by negative selection. Unwanted cells (CD11b+ CD11c+ Gr-1+ Ter-119+ CD19+ CD8a+ cells) were targeted for removal with biotinylated antibodies (BioLegend), streptavidin-coated magnetic particles (RapidSpheres) and EasySep magnet (STEMCELL), and followed by staining with mCD1d/PBS-57 and anti-TCR. Then, iNKT cells were sorted with BD FACSAria III (BD Biosciences), and total RNA was isolated from sorted cells according to the manufacturer’s instructions using the RNeasy plus micro kit (Qiagen). RNA-Seq library preparation was performed using the Illumina TruSeq Stranded mRNA Kit, according to manufacturer’s instructions, and sequenced with Illumina HiSeq 2000 Sequencer. Read quality was confirmed using FastQC v0.10.1 before alignment using TopHat v2.0.10 on the mouse GRCm38/mm10 genome.
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| Contributor(s) |
Lu Y, Veillette A |
| Citation(s) |
30833791 |
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| Submission date |
Aug 16, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
André Veillette |
| Organization name |
Institut de Recherches Cliniques de Montréal
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| Street address |
110 avenue des pins ouest
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| City |
Montreal |
| State/province |
Québec |
| ZIP/Postal code |
H2W1R7 |
| Country |
Canada |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA486367 |
| SRA |
SRP158145 |
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