|
| Status |
Public on Mar 16, 2021 |
| Title |
UTX CUT&Tag Utx-/- CD8+ T cells D15 Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Utx-/- CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
timepoint: 15 days post infection
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 or CUT&Tag).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted using TRIZOL reagent, followed by mRNA purification
Libraries were generated using KAPA mRNA HyperPrep Kit (KK8580) for RNA-seq, KAPA HyperPrep Kit (KK8504) for CUT&RUN, or PCR amplification for CUT&Tag
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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.
CUT&RUN or CUT&Tag aligment to the mm9 or ecoli genome was performed using Bowtie2, CUT&Tag with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1500
CUT&Tag bigwig files generated from merged bam files with deepTools options: bamCoverage --ignoreDuplicates
CUT&RUN peaks called with MACS2 and hiddenDomains CUT&Tag peaks called with MACS2 on merged bamfiles with options: --broad --broad-cutoff 0.1
CUT&Tag UTX peaks were merged from D0 and D15 timepoints, and filtered for blacklisted regions and RPKM > 1
CUT&Tag UTX peak readcounts for individual bam files were counted with deepTools: multiBamSummary --outRawCounts --ignoreDuplicates
EdgeR identified significant UTX peaks between D15 WT vs. D0 WT or D15 WT vs. D15 KO with mapped reads per ecoli reads normalization factors
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with reads per gene (RNA-seq) or peak (CUT&RUN or CUT&Tag)
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 16, 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 |
GPL24247 |
| Series (1) |
| GSE143736 |
UTX constrains antiviral CD8+ T cell responses during chronic virus infection |
|
| Relations |
| BioSample |
SAMN18311347 |
| SRA |
SRX10341617 |
