|
| Status |
Public on Aug 25, 2017 |
| Title |
Input DNA in lytic cells |
| Sample type |
SRA |
| |
|
| Source name |
TREx-F3H3-K-Rta BCBL-1 cells
|
| Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
| Characteristics |
pathogen: KSHV
tissue: peritoneal effusion
cell type: KSHV positive B cell lymphoma
passages: 5~10
chip antibody: none
|
| Growth protocol |
TREx-F3H3-K-Rta BCBL-1 cells were grown in RPMI 1640 medium supplemented with 15% fetal calf serum (FBS). Cells were treated with or without 1 µg/mL doxycycline for 24 h
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin DNA from 1 X 108 cells was used per immunoprecipitation assay with 10 µg of ZIC2 antibody
ChIP-enriched and input DNA samples were used to generate Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KR0453) according to manufacturer’s recommendations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
Data were trimmed by Trimmomatic trimming tool
The ChIP-Seq data (FASTQ sequence reads) was aligned to human hg19 reference genome and reference KSHV genome sequence (Human herpesvirus 8 strain JSC-1 clone BAC16, GenBank: GQ994935.1) with Bowtie 2
Peak finding was performed with the MACS2 program following the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
Genome_build: hg19 + KSHV genome (GQ994935.1)
Supplementary_files_format_and_content: MACS2 generated bed file
|
| |
|
| Submission date |
Aug 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoshihiro Izumiya |
| E-mail(s) |
yizumiya@ucdavis.edu
|
| Organization name |
UC Davis Medical Center
|
| Street address |
4645 Second Avenue
|
| City |
sacramento |
| ZIP/Postal code |
95817 |
| Country |
USA |
| |
|
| Platform ID |
GPL23888 |
| Series (1) |
| GSE102462 |
ZIC2 ChIP-Seq in KSHV latent and lytic reactivated BCBL-1 cells |
|
| Relations |
| BioSample |
SAMN07487361 |
| SRA |
SRX3082737 |
