|
| Status |
Public on Apr 24, 2017 |
| Title |
24hInd Input (iSLK-Bac16WT cells) |
| Sample type |
SRA |
| |
|
| Source name |
iSLK-Bac16WT cells
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
cell type: KSHV positive iSLK endothelial cells derived from gingival KS lesion
genotype/variation: RTA protein is under tet-inducible promoter
treatment: induced with doxycycline for 24h to trigger lytic reactivation
chip antibody: none
|
| Treatment protocol |
Cells were induced for lytic reactivation by Doxycycline for 24h.
|
| Growth protocol |
iSLKBac16WT cells were grown in DMEM medium supplemented with 10%FBS 1ug/ml puromycin, 250 ug/ml G418, and 600 ug/ml hygromycin B
|
| 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
ChIP DNA was used for library prepartation for ChIP-seq analysis
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DNA extracted from the sonicated chromatin
|
| 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 database to 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 24, 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 |
| GSE98087 |
Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (iSLKBac16WT ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN06820784 |
| SRA |
SRX2754557 |
