|
| Status |
Public on Feb 25, 2021 |
| Title |
Pofut1_KO2 |
| Sample type |
SRA |
| |
|
| Source name |
sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Pofut1 KO
cell type: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen
strain: C57BL/6
|
| Growth protocol |
P14 cells transduced with indicated sgRNAs were sorted from spleen after LCMV-Armstrong infection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Pofut1_ATAC_summarizedCounts.tsv.gz
|
| Data processing |
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Hongbo Chi |
| E-mail(s) |
hongbo.chi@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE160313 |
In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions [Pofut1 ATAC-seq] |
| GSE160341 |
In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions |
|
| Relations |
| BioSample |
SAMN16581695 |
| SRA |
SRX9389522 |
