|
| Status |
Public on Feb 09, 2021 |
| Title |
CUT&RUN WT CD8+ T cells Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
WT CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time point: 15 days post infection
agent: chronic lymphocytic choriomeningitis virus
genotype: wild-type
antibody: H3K27me3
|
| 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P14_D15_K27me3_WT_merge.bw
P14_D15_K27me3_WT_merge_hidden_mapq_10_analysis.bed
P14_D15_K27me3_WT_merge_hidden_mapq_10_vis.bed
P14_D15_K27me3_WT_merge_macs2_broadPeaks.bed
|
| Data processing |
Library strategy: CUT&RUN
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 09, 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 |
GPL19057 |
| Series (1) |
| GSE143736 |
UTX constrains antiviral CD8+ T cell responses during chronic virus infection |
|
| Relations |
| BioSample |
SAMN13867597 |
| SRA |
SRX7568509 |
