|
| Status |
Public on Mar 17, 2020 |
| Title |
Lytic_GROseq |
| Sample type |
SRA |
| |
|
| Source name |
TRExBCBL1-RTA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TRExBCBL1-RTA
infection: KSHV
replication: Lytic
|
| Treatment protocol |
1ug/ml doxycycline for 24 h
|
| Growth protocol |
RPMI1640 + 10% FBS + 1% Pen/Strep + 20ug/ml Hygromycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We followed a previous published protocol (Li et al., 2015 Mol Cell)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: GRO-seq
Reads were trimmed based on quality score from both ends using Partek Flow and aligned to hg19 genome using bowtie 2. Peak calling and annotation done using HOMER (-style groseq)
Reads were trimmed based on quality score from both ends using Partek Flow
Reads were aligned to hg19 genome using bowtie 2
(ChIP-Seq) Peak calling was done using HOMER (H3K27ac peaks used -size 1000)
(ChIP-Seq) Peak annotation was done using HOMER; TSS peaks were removed
(ChIP-Seq) Motif analysis was done using HOMER
(ChIP-Seq) Heatmaps and profiles were generated using NGSPlot (-SC global, -G hg19, -L 10000)
(ChIP-Seq) Potential superenhancers were identified using HOMER (-sytle super)
(4C-Seq) Genomic interactions were identified using 4cseqpipe (hg19 genome used; -stat_type linear_mean -trend_resolution 1000)
(GROSeq) Peak calling and annotation done using HOMER (-style groseq)
(GROSeq) NGSPlot used to generate heatmaps and profiles (-SC global, -G hg19, -L 10000)
Genome_build: hg19
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Mar 16, 2020 |
| Last update date |
Mar 17, 2020 |
| Contact name |
Angela Park |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Southern California
|
| Department |
Molecular Microbiology and Immunology
|
| Street address |
1501 San Pablo St, ZNI 521
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL27467 |
| Series (1) |
| GSE147063 |
Global epigenomic analysis of primary effusion lymphoma identifies MYC super-enhancers and enhancer RNAs associated with KSHV infection |
|
| Relations |
| BioSample |
SAMN14384526 |
| SRA |
SRX7918805 |
