|
Status |
Public on Feb 16, 2019 |
Title |
HA-Input-Rep2 |
Sample type |
SRA |
|
|
Source name |
Cell culture
|
Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
Characteristics |
cell line: iSLK latent infection: HA-ORF34 time point: 48 hr chip antibody: None
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were lysed, nuclei were isolated and sonicated to fragment chromatin which was used for immunoprecipitation with the indicated antibody. Libraries were prepared using the Swift Biosciences protocol.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
iSLK-HA-ORF34 Genomic and viral DNA
|
Data processing |
Reads were analyzed using FastQC and adapters were trimmed with TrimGalore. Trimmed reads were aligned using Bowtie2 alignment program. The aligned reads were converted to BAM files, filtered with a q cutoff of 10 and sorted using SAMTools. The sorted files were converted to tdf using IGV. Genome_build: hg19 (GRCh37), GQ994935.1 Supplementary_files_format_and_content: *tdf: tdf files for each sample.
|
|
|
Submission date |
Feb 14, 2019 |
Last update date |
Feb 17, 2019 |
Contact name |
Britt Glaunsinger |
Organization name |
UC Berkeley
|
Street address |
565 Li Ka Shing Center
|
City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
|
|
Platform ID |
GPL25719 |
Series (2) |
GSE126601 |
Genome-wide map of viral transcription factor ORF34 binding in Kaposi's Sarcoma Herpesvirus (KSHV) |
GSE126603 |
An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus |
|
Relations |
BioSample |
SAMN10953172 |
SRA |
SRX5382895 |