|
| Status |
Public on Dec 21, 2020 |
| Title |
Tr1_Prdm1 cKO_2 |
| Sample type |
SRA |
| |
|
| Source name |
Tr1 cells derived in vitro with IL-27
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: CD4 Cre(+/-); Prdm1 f/f
|
| Growth protocol |
Naïve CD4 T cells were polarized to Tr1 cells with anti-CD3 (1ug/ml) and anti-CD8 (1ug/ml) stimulation in the presence of IL-27 (25ng/ml) for 72h
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
6,000 viable Tr1 cells were sorted for each sample and frozen in BambankerTM cell freezing media (LYMPHOTEC Inc.) at -80℃.
For ATAC-seq library preparation, cells were thawed at 37℃, washed once with PBS, and lysed and tagmented in 1X TD Buffer, 0.2ml TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS in 40ml reaction volume following the protocol described by Corces at al. (Corces et al., 2016). The DNA was purified immediately with the MinElute PCR purification kit (QIAGEN), and then PCR amplified and quantified as we previously described (Wallrapp et al., 2019). The library was sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
ATAC-seq
Tr1_70hr_98_16.R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
|
| Data processing |
ATAC-seq data were processed using a public pipeline (Lee et al., 2016). Briefly, reads were aligned to the mm10 genome using Bowtie2 and filtered to remove duplicates and mitochondrial reads. Biological replicate for each group were merged peaking-calling using MACS2 (Zhang et al., 2008)
Genome_build: mm10
Supplementary_files_format_and_content: Format: bigwig, Content: signal track for fold change generated by Macs2
|
| |
|
| Submission date |
Sep 28, 2020 |
| Last update date |
Dec 21, 2020 |
| Contact name |
Vijay Kuchroo |
| Organization name |
Brigham & Women's Hospital
|
| Department |
Neurology
|
| Lab |
Kuchroo
|
| Street address |
60 Fenwood Road
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE158701 |
IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets[Prdm1/Maf KO Tr1 ATAC-seq] |
| GSE159208 |
IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets |
|
| Relations |
| BioSample |
SAMN16283911 |
| SRA |
SRX9208549 |
