|
| Status |
Public on Jun 14, 2017 |
| Title |
12hInd-IgG ChIP |
| Sample type |
SRA |
| |
|
| Source name |
TRExBCBL1-RTA cells
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
tissue: KSHV infected Body Cavity Based Lymphoma Cells
treatment: RTA protein is under tet-inducible promoter
antibody: Control IgG Antibody (Cell Signaling Technology #2729)
|
| Treatment protocol |
Cells were induced for lytic reactivation by Doxycycline for 24h.
|
| Growth protocol |
TRExBCBL1-Rta cells were grown in RPMI medium with 10% FBS. Uninduced cells were grown using 10% Tet-free 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 anti-H4R3symmtreic antibody by following standard ChIP protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control IgG ChIP DNA
|
| Data processing |
The libraries were run on Illumina Next-Seq 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 database to determine the DNA bound by H4R3sym histone H4
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 |
Jun 14, 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) |
| GSE98058 |
Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome |
| GSE100044 |
Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (H4R3me2s ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN07237976 |
| SRA |
SRX2919006 |
