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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.
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|
|
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
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|
|
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 |