|
| Status |
Public on Nov 13, 2017 |
| Title |
BZLF1 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell line: GM12878
chip antibody: anti-BZLF1 antibody BZ1 (Santa Cruz, sc-53904, lot 2313)
|
| Biomaterial provider |
https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&product=CC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BZLF1 and EBNA1 ChIPs were performed as previously described (Keck et al., submitted) using 3 µg of the anti-BZLF1 antibody BZ1 (Santa Cruz, sc-53904, lot 2313) and 3 µg of the anti-EBNA1 antibody 0211 (Santa Cruz, sc-57719, lot K2013).
We prepared deep sequencing libraries 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 2500 |
| |
|
| Data processing |
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
Peaks were visualized after normalization to the background baseline
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 |
Apr 24, 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 |
GPL23185 |
| Series (2) |
| GSE98121 |
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [ChIP-seq] |
| GSE98123 |
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation |
|
| Relations |
| BioSample |
SAMN06821428 |
| SRA |
SRX2755182 |
