|
| Status |
Public on Feb 09, 2021 |
| Title |
RNA-seq Utx-/- CD8+ T cells Rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
Utx-/- CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point: 21 days post infection
agent: chronic lymphocytic choriomeningitis virus
genotype: Utx-/- knock-out
|
| Treatment protocol |
WT or Utx-/- P14+CD8+ T cells were transferred to C57BL/6 recipient mice, CD4+ T cells were depleted prior to LCMV-A22 infection, and donor P14+CD8+ T cells were sorted from spleens at day 21 post-infection (RNA-Seq) or 15 days post-infection (CUT&RUN).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZOL reagent, followed by mRNA purification
Libraries were generated using KAPA mRNA HyperPrep Kit (KK8580) for RNA-seq or KAPA HyperPrep Kit (KK8504) for CUT&RUN
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Initial processing and basecalling was done using Genome Analyzer Pipeline Software
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
RNA-seq alignment to the mm9 genome was performed using Tophat2
RNA-seq reads were counted at mm9 genes using HTseq-count
CUT&RUN aligment to the mm9 genome was performed using Bowtie2
CUT&RUN peaks called with MACS2 and hiddenDomains
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with reads per gene (RNA-seq) or peak (CUT&RUN)
|
| |
|
| Submission date |
Jan 15, 2020 |
| Last update date |
Feb 10, 2021 |
| Contact name |
Joshua Starmer |
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Lab |
Magnuson
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE143736 |
UTX constrains antiviral CD8+ T cell responses during chronic virus infection |
|
| Relations |
| BioSample |
SAMN13867599 |
| SRA |
SRX7568507 |
