|
| Status |
Public on May 07, 2024 |
| Title |
Jurkat cells, PMA Ionomycin, 8 hours, p300 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood mononuclear cells
cell line: Jurkat E6-1
cell type: T cells
genotype: WT
treatment: PMA Ionomycin
|
| Treatment protocol |
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals) where specified. 1 uM S109, 1 uM SP100030, or 10 uM C646 were co-treated for 8 hours (S109, SP100030) or 24 hours (C646)
|
| Growth protocol |
Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies. Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation.
CUT&RUN libraries were prepared using NEBNext DNA Ultra II Library Prep kit according to manufacturer instructions. Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB E7104S)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
p300 antibody
|
| Data processing |
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.5.0.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.4
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.5.2
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Yi Fan Chen |
| E-mail(s) |
yxc1272@case.edu
|
| Organization name |
Case Western Reserve University School of Medicine
|
| Street address |
2109 Adelbert Road Biomedical Research Building 747A
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE244396 |
Binding Changes in Chromatin Factors Upon Targeted XPO1 Inhibition in T Cells |
|
| Relations |
| BioSample |
SAMN40201596 |
| SRA |
SRX23794243 |
