|
| Status |
Public on Sep 18, 2017 |
| Title |
Iono R2 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat T cells
|
| Organism |
Homo sapiens |
| Characteristics |
jurkat clone: A3
genotype: WT
|
| Treatment protocol |
Cells were treated with either 20 ng/ml PMA, 1 ug/ml Ionomycin, or 20 ng/ml PMA and 1 ug/ml Ionomycin for 3 hours.
|
| Growth protocol |
Jurkat A3 T cells were routinely sub-cultured by plating 5 x 10^5 cells into a T75 flask every other day. Cells were cultured in RPMI media supplemented with 1% L-glutamine and 10% foetal calf serum. Cells were maintained at 37 degrees celcius and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from 50,000 cells using Nuclei EZ Lysis Buffer (Sigma-Aldrich).
ATAC libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
1 ug/ml Iono for 3 hrs
|
| Data processing |
Bowtie2 using to align trimmed paired-end data and single-ended read data to the hs37d5 reference genome.
ATAC-seq peaks were identified using cisGenome, and peak sizes were claculated by determining the number of fragment ends that were located within each peak for each of the samples. Data was normlised by the linrary size for each sample.
Peak detection and coverage track generation were performed using MACS on merged replicates. Coverage tracks were uploaded to the UCSC Genome Browser.
Tag counts were normalized using centre-scaling, and sorted on log2 treatment/control fold change.
genome build: hs37d5
processed data files format and content: Data include all counts per peak per sample. A separate spreedsheet includes normalised peak counts per condition (of pooled replicates) used in the analyses.
|
| |
|
| Submission date |
Nov 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nigel Paul Dyer |
| E-mail(s) |
nigel.dyer@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Street address |
Gibbet Hill Road
|
| City |
Coventry |
| ZIP/Postal code |
CV4 7AL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE90718 |
Integration of kinase and calcium signaling at the level of chromatin underlines inducible gene activation in T cells |
|
| Relations |
| BioSample |
SAMN06077187 |
| SRA |
SRX2384384 |
