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Sample GSM941712 Query DataSets for GSM941712
Status Public on Jun 02, 2012
Title KSHV LANA_ChIPSeq
Sample type SRA
 
Source name BCBL1 pleural effusion lymphoma, KSHV LANA ChIP
Organism Human gammaherpesvirus 8
Characteristics cell line: BCBL1
cell type: KSHV-infected pleural effusion lymphoma cells
chip antibody: rat anti-KSHV LANA
antibody vendor: Advanced Biotechnologies
antibody catalog #: 13-210-100
antibody lot#: A0811
Treatment protocol According to the publication "Chromatin immunoprecipitation and microarray-based analysis of protein location" from the Natural Protocol (PMID 17406303).
Growth protocol BCBL1 cells were grown to 1x10^6 cells/ml in RPMI with 10% FBS supplemented with Glutamax and Penn/Strep.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description KSHV
Data processing Alignment: Alignment was performed using Bowtie software on both the human HG18 genome downloaded from the UCSC browser site and the viral genome HQ404500BAC36 with a 35 repeat added to terminal.
Wiggle files were created using moving average of raw reads at each base. Peaks were identified on wiggle profile based on Mathematical maxima in local regions.
Supplementary_files_format_and_content: WIG: Single-column UCSC Wiggle file format.
Supplementary_files_format_and_content: BED: Six-column peak bed format.
Genome_build: HQ404500BAC36 with 35 repeat added to terminal
 
Submission date Jun 01, 2012
Last update date Jun 11, 2013
Contact name Priyankara J Wickramasinghe
E-mail(s) priyaw@wistar.org
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL15642
Series (1)
GSE38411 Cohesins Repress KSHV Immediate Early Gene Transcription During Latency
Relations
BioSample SAMN02197551

Supplementary file Size Download File type/resource
GSM941712_KSHV_Peak.bed.gz 521 b (ftp)(http) BED
GSM941712_average_kshv.wig.gz 128.9 Kb (ftp)(http) WIG
Processed data provided as supplementary file
Raw data not provided for this record

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