|
| Status |
Public on Feb 16, 2019 |
| Title |
HA-ChIP-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: HA-Tag (C29F4) (Cell Signaling)
|
| 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 |
SAMN10953175 |
| SRA |
SRX5382893 |
