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Sample GSM2668641 Query DataSets for GSM2668641
Status Public on Jun 14, 2017
Title Und-Input
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: none (input)
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 DNA extracted from the sonicated chromatin
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 SAMN07237974
SRA SRX2919001

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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