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Sample GSM3609584 Query DataSets for GSM3609584
Status Public on Feb 16, 2019
Title HA-Input-Rep2
Sample type SRA
 
Source name Cell culture
Organisms Homo sapiens; Human gammaherpesvirus 8
Characteristics cell line: iSLK
latent infection: HA-ORF34
time point: 48 hr
chip antibody: None
Extracted molecule genomic DNA
Extraction protocol Cells were lysed, nuclei were isolated and sonicated to fragment chromatin which was used for immunoprecipitation with the indicated antibody.
Libraries were prepared using the Swift Biosciences protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description iSLK-HA-ORF34
Genomic and viral DNA
Data processing Reads were analyzed using FastQC and adapters were trimmed with TrimGalore.
Trimmed reads were aligned using Bowtie2 alignment program.
The aligned reads were converted to BAM files, filtered with a q cutoff of 10 and sorted using SAMTools.
The sorted files were converted to tdf using IGV.
Genome_build: hg19 (GRCh37), GQ994935.1
Supplementary_files_format_and_content: *tdf: tdf files for each sample.
 
Submission date Feb 14, 2019
Last update date Feb 17, 2019
Contact name Britt Glaunsinger
Organization name UC Berkeley
Street address 565 Li Ka Shing Center
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL25719
Series (2)
GSE126601 Genome-wide map of viral transcription factor ORF34 binding in Kaposi's Sarcoma Herpesvirus (KSHV)
GSE126603 An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus
Relations
BioSample SAMN10953172
SRA SRX5382895

Supplementary file Size Download File type/resource
GSM3609584_HA_Input_Human_R2.tdf 360.8 Mb (ftp)(http) TDF
GSM3609584_HA_Input_KSHV_R2.tdf 227.2 Kb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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