|
| Status |
Public on Sep 05, 2013 |
| Title |
KSHV-BJAB |
| Sample type |
SRA |
| |
|
| Source name |
KSHV-Infected BJAB Cell Line
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
cell line: KSHV-BJAB
host: Human B-Cells
sequenced molecule: Viral and Human Genomic DNA
|
| Treatment protocol |
~1.0e7 cells were cross-linked with formaldehyde (final concentration 1%) for 5 minutes and quenched for 5 minutes with 125mM Glycine
|
| Growth protocol |
Latent KSHV-infected lymphoma cell lines (BC1, BCBL1, and KSHV-BJAB) were cultured in RPMI 1640 supplemented with 100 ug/mL streptomycin sulfate, 100 U/mL penicillin G (Life Technologies), 2mM L-glutamine, 0.05mM 2-mercaptoethanol, 0.075% sodium bicarbonate, 1 U/mL IL-6 (PeproTech Inc), and 10% FBS and were maintained at 37°C in 5% CO2. KSHV-BJAB cells were also maintained under 0.2-mg/mL hygromycin selection. Latent KSHV-infected endothelial L1-TIVE cells were grown in Dulbecco modified Eagle medium (DMEM) supplemented with 100 ug/mL streptomycin sulfate and 100 U/mL penicillin G and 5% FBS. Latently infected KSHV-human umbilical vein endothelial cells (HUVEC) were cultured in endothelial growth medium (EGM-2; Clonetics) supplemented with 0.5 ug/mL puromycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed, and then sonicated to shear DNA to an average fragment length of 200 to 400 bp. Sheared DNA was then collected by phenol-chloroform extraction.
FAIRE-enriched DNA was then prepared for sequencing using the Illumina Truseq DNA Sample Preparation Kit V2 (Illumina) per the manufacturer’s instructions or was prepared by the UNC High-Throughput Sequencing Facility (BCBL1 and non-cross-linked BCBL1 control)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KSHV-Infected BJAB Cell Line
|
| Data processing |
Library strategy: FAIRE-seq
CASAVA v1.8.2 for BC1, KSHV-BJAB, KSHV-HUVEC, L1-TIVE. CASAVA v1.7 for BCBL1 samples
Reads were filtered using TagDust
Reads were aligned to NC_009333 using Bowtie. Reads were permitted to align to up to four locations in the genome, but the single best possible alignment was chosen.
Regions with significantly enriched FAIRE signal were differentiated from background using MACS2 assuming the average fragment length was 250bp.
Genome_build: NC_009333.1
Supplementary_files_format_and_content: BED formatted file containing peak locations on NC_009333.1 and the -log10 q-value.
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
May 12, 2023 |
| Contact name |
Ian Jonathan Davis |
| E-mail(s) |
ian_davis@med.unc.edu
|
| Phone |
919-966-5360
|
| Organization name |
University of North Carolina
|
| Department |
Genetics, Pediatrics
|
| Street address |
450 West Drive
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL17680 |
| Series (1) |
| GSE50581 |
The Open Chromatin Landscape of Kaposi's Sarcoma-Associated Herpesvirus |
|
| Relations |
| BioSample |
SAMN02344573 |
| SRA |
SRX344572 |
