|
| Status |
Public on Feb 13, 2020 |
| Title |
ATAC_D2_S2 |
| Sample type |
SRA |
| |
|
| Source name |
Th17
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: None
donor: 2
day: Day 4
cell type: Th17
|
| Treatment protocol |
Cells were treated with either DMSO or GSK-J4 for 48 hours following differentiation.
|
| Growth protocol |
Briefly, naïve CD4+ CD45RA+ T cells were purified from PBMCs of healthy donors with T-cell enrichment kit (Miltenyi) and then cultured in the presence of anti-CD3/CD28 activation beads (1:20 bead to cell ratio) (Invitrogen) plus polarization condition medium of RPMI-1640 containing 10% knockout serum replacement (ThermoFisher) supplemented with the following cytokines at 37C for 6 days. Naïve T cells were cultured in the presence of IL-1b (20 ng/ml, Peprotech), IL-6 (20 ng/ml, Peprotech), recombinant TGF-b (3 ng/ml, Peprotech) and IL-23 (10 ng/ml) (R & D) for 7 days. For Th17 cell expansion
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as described in Buenrostro et al. 2013.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment was performed using bowtie2 v2.3.4.1.
Peak calling was performed using MACS2 v2.1.0.
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Feb 13, 2020 |
| Contact name |
Adam Cribbs |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
NDORMS
|
| Street address |
Windmill Road
|
| City |
Oxford |
| ZIP/Postal code |
OX37LD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE127767 |
Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism |
| GSE128008 |
Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism [III] |
|
| Relations |
| BioSample |
SAMN11082974 |
| SRA |
SRX5493464 |
