|
| Status |
Public on Aug 08, 2023 |
| Title |
ITK-SYK+ CD4+ T cells PD1 KO ex vivo replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
primary cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: primary cells
cell type: ITK-SYK+ CD4+ T cells
genotype: PD1 KO
treatment: ex vivo
time: Day 5 post TAM
|
| Treatment protocol |
For the ATAC-seq experiments involving inhibitor incubation, single-cell suspensions were generated from spleens of acutely induced ITK-SYKCD4-creERT2, or ITK-SYKCD4-creERT2;Pdcd1-/- mice.
Next, the cells were incubated in vitro for three hours in presence of 5 μM ACLY inhibitor BMS-303141 or DMSO. Finally, ITK-SYK expressing eGFP+ cells were FACS-sorted and immediately processed for ATAC-seq.
|
| Growth protocol |
ITK-SYKCD4-creERT2 or ITK-SYKCD4-creERT2;Pdcd1-/- mice received a single dose of 2 mg tamoxifen. Five days after injection, single-cell suspensions were generated from the spleens and 50,000 eGFP+ FACS-sorted cells were used for the transposase reaction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The transposase reaction was performed as previously described (M.R. Corces et al. Nat Methods 2017).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
chromVAR_exvivo.txt
|
| Data processing |
Cutadapt (v3.1) was used to remove adapter sequences. Reads were aligned to the mm9 genome using Bowtie2.
Duplicates were marked with MarkDuplicates (Picard, v2.24.0) and removed with Samtools (v1.11). To filter properly mapped reads, we used Samtools with the following options: exclude multi-mapped reads (MAPQ < 30) and reads with flag 1796 or 1804.
Samtools with option “-f 2” was used to filter properly paired reads. Adjustment using the Tn5 shift was performed with alignmentSieve (deepTools (v3.3.2)).
Next, we filtered for nucleosome-free reads (0-100 bp). Visual inspection after filtering was performed using the bamPEFragmentSize function from deepTools (v3.3.2).
Next, we used MACS2 (v2.2.7.1) to call ATAC-seq peaks with the following parameters: –nomodel –nolambda –keep-dup auto -call-summits. chromVAR (v1.14.0) was used to calculate motif scores.
Assembly: mm9
Supplementary files format and content: tab-delimited text file include counts values for each Sample
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Tim Wartewig |
| E-mail(s) |
tim.wartewig@yale.edu
|
| Phone |
2034354232
|
| Organization name |
TUM
|
| Department |
Clinical Chemistry
|
| Lab |
Ruland Lab
|
| Street address |
Einsteinstrasse 25
|
| City |
Munich |
| ZIP/Postal code |
81675 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE213180 |
PD-1 instructs a tumor suppressive metabolic program to restrain AP-1 activity in T cell lymphoma [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN30809998 |
