|
| Status |
Public on Jun 30, 2017 |
| Title |
ChIP-seq_BRD4_Mutu_100E6_vehicle_Replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
MutuI (EBV+ Burkitt lymphoma cell line)
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell line: MutuI
pathogen: Epstein-Barr virus
chip antibody: BRD4
|
| Treatment protocol |
Unless noted, cells were not treated. For Mutu ChIPs with 100E6 cells, cells were treated with either 1 uM JQ1 or vehicle for 24 hours, and then cells were fixed for ChIP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Unless noted, 18E6 cells were collected for ChIP. For the Mutu cells treated with JQ1 or vehicle, 100E6 cells were collected for ChIP.
DNA was prepared and ChIP performed as described in the paper
ChIP-seq libraries were prepared as described in the paper
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
Peaks were visualized after normalization to the background baseline
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html. Wig columns are chromosome, start, stop, counts per million mapped reads.
|
| |
|
| 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) |
| GSE84213 |
BET proteins bind the lytic origins of replication [MutuI ChIP-seq] |
| GSE84214 |
BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps |
|
| Relations |
| BioSample |
SAMN06927264 |
| SRA |
SRX2795362 |
