|
| Status |
Public on Jun 30, 2017 |
| Title |
ChIP-seq_BRD4_AkataZta_acy_JQ1_LGNFR-_Replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Akata-Zta cells
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell line: Akata-ZTA
pathogen: Epstein-Barr virus
chip antibody: BRD4
|
| Treatment protocol |
Log-phase cultures were pretreated with 1) 200 μM acyclovir (Sigma-Aldrich) and 2) either 1 uM JQ1 or vehicle (DMSO) for 1 hr before induction with 500 ng/mL doxycycline (Sigma-Aldrich). After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotec).
|
| Growth protocol |
Cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech) in 5% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
18E6 cells were collected, and ChIP was performed as described in the paper.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
May 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
JJ Miranda |
| E-mail(s) |
jmiranda@barnard.edu
|
| Organization name |
Barnard College, Columbia University
|
| Street address |
3009 Broadway
|
| City |
New York |
| ZIP/Postal code |
10027 |
| Country |
USA |
| |
|
| Platform ID |
GPL23362 |
| Series (2) |
| GSE84214 |
BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps |
| GSE98773 |
JQ1 prevents BRD4 recruitment to the lytic origins of replication [Akata-Zta Brd4 ChIP-seq] |
|
| Relations |
| BioSample |
SAMN06927269 |
| SRA |
SRX2795369 |
