|
| Status |
Public on Apr 22, 2017 |
| Title |
24hInd ORF59 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
cells were induced with doxycycline for 24h
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
tissue: KSHV infected Body Cavity Based Lymphoma Cells
genotype/variation: RTA protein is under tet-inducible promoter
antibody: ORF59 Antibody: Custom synthesized for our lab - anti-KSHV-ORF59 antibody from GenScript
|
| Treatment protocol |
Cells were induced for lytic reactivation by Doxycycline for 12h or 24h.
|
| Growth protocol |
TRExBCBL1-Rta cells were grown in RPMI medium with 10% FBS. Uninduced samples were grown with Tet-Free 10%FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Latent and lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
Chromatins were immunoprecipitated using specific listed antibody by following standard ChIP protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ORF59 ChIP
|
| Data processing |
The libraries were run on Illumina NextSeq500 instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Genomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the KSHV genome databaseto determine the DNA bound by specific targets
ChIP peaks were calculated using CLC workbench ChiP-peak tool using input as reference
Genome_build: NCBI genome build of KSHV sequence accession# NC_009333
Supplementary_files_format_and_content: ChIp peaks on the viral genomes are in wig file (CLC workbench)
|
| |
|
| Submission date |
Apr 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Subhash C Verma |
| E-mail(s) |
scverma@medicine.nevada.edu
|
| Phone |
775-682-6743
|
| Organization name |
University of Nevada, Reno
|
| Department |
Microbiology and Immunology
|
| Lab |
Verma Lab
|
| Street address |
1664 N Virginia Street, MS 320
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL23366 |
| Series (2) |
| GSE98057 |
Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (TREx Und 12h 24hInd ChIP-Seq) |
| GSE98058 |
Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome |
|
| Relations |
| BioSample |
SAMN06808403 |
| SRA |
SRX2751817 |
