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| Status |
Public on Dec 04, 2020 |
| Title |
Whole genome transcriptome of in vivo Treg cells and ex vivo TGF-beta induced Treg cells from WT and Aim2 knockout mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To understand the whole genome transcriptome of in vivo Treg cells and ex vivo TGF-beta induced Treg cells from WT and Aim2 knockout mice, the total RNA was extracted from indicated Treg cells using the Direct-zol miniprep kit (Zymo Research, R2060). The RNA samples were firstly enriched by Oligo(dT) magnetic beads and used to construct BGISEQ-500 libraries. RNA-seq libraries sequenced using the 50bp single-end protocol (in vivo isolated Treg cells) or 100bp paired-end protocol (TGF-β induced Treg cells) via the BGISEQ-500 sequencer per the manufacturer’s protocol. After filtering of adaptors and low quality reads, clean reads (>26 Million reads per sample for in vivo isolated Treg cells and >40 Million reads per sample for TGF-β induced Treg cells) are mapped to mouse reference genome using HISAT /Bowtie2 tool. Mapping results are stored in BAM files using SAMtools. Total read counts in gene level were summarized using featureCounts function in the Rsubread in R environment, with the R package biomaRt for gene and transcripts mapping. The differential expression (DE) genes were analyzed by DESeq2 package with default setting using total read counts as input, and the adjusted p value (padj) less than 0.05.
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| Overall design |
Examination of differential gene expression of in vivo islolated Treg cells with or without 24-hour TCR stimulation and TGF-beta induced Treg (iTreg) cells at day one from naive CD4 T cells in WT and Aim2 knockout mice.
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| Contributor(s) |
Chou W, Guo Z, Tan X, Ting JY |
| Citation(s) |
33505023 |
| |
| Submission date |
Jun 19, 2019 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Zengli Guo |
| E-mail(s) |
[email protected]
|
| Phone |
919-966-5950
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| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Lineberger Comprehensive Cancer Center
|
| Street address |
125 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platforms (1) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA549699 |
| SRA |
SRP201902 |
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