|
| Status |
Public on May 11, 2020 |
| Title |
ATAC-Seq TexProg1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
treatment: LCMV Clone 13 infection
|
| Treatment protocol |
Sorted cells (2.5-to-5x104) were washed twice in cold PBS and resuspended in 50μl of cold lysis buffer (10nM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween).
|
| Growth protocol |
At D30 p.i. with Cl13, CD8 T cells were isolated from spleens of infected recipients
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were centrifuge (750xg, 10min, 4oC) and nuclei were resuspended in 50μl of transposition reaction mix (TD buffer [25μl], Tn5 Transposase [2.5μl], nuclease-free water [22.5μl]; (Illumina)) and incubated for 30min at 37oC.
Transposed DNA fragments were purified using a Qiagen Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina) and amplified by PCR for 11 cycles using NEBNext High Fidelity 2x PCR Master Mix (New England Biolabs). PCR products were purified using a PCR Purification Kit (Qiagen) and amplified fragments size was verified on a 2200 TapeStation (Agilent Technologies) using High Sensitivity D1000 ScreenTapes (Agilent Technologies). Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
TexProg1_rep2
|
| Data processing |
fastq files were aligned to GRCm38/mm10 reference genome using bowtie2
Samtools/bedtools were used to process and filter mitochondrial reads and to remove duplicates.Peak calling was performed using MACS v2 (FDR q-value 0.01).
differential expression analysis was run using DESeq 2 package and data normalized
Differentially accessible regions were identified following DESeq2 normalization using an FDR cut-off < 0.05 or 0.01 or otherwise indicated
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts
|
| |
|
| Submission date |
May 05, 2020 |
| Last update date |
May 12, 2020 |
| Contact name |
E JOHN WHERRY |
| Organization name |
University of Pennsylvania
|
| Department |
Systems Pharmacology and Translational Therapeutics,Institute for Immunology
|
| Street address |
421 Curie Blvd,354 BRB II/III
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE149877 |
Epigenetic landscape of four exhausted CD8 T cell subsets |
| GSE149879 |
Landscape of four exhausted CD8 T cell subsets |
|
| Relations |
| BioSample |
SAMN14833846 |
| SRA |
SRX8248219 |
