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Sample GSM1958047 Query DataSets for GSM1958047
Status Public on Dec 16, 2015
Title H3K27me3 CHIP-seq in LCL
Sample type SRA
 
Source name LCL cell line
Organism Homo sapiens
Characteristics cell line: LCL
cell type: EBV positive B-cells
chip antibody: H3K27me3
chip antibody vendor: Active Motif
chip antibody cat. #: 39155
chip antibody lot #: 1613015
Treatment protocol Cells were maintained and isolated in logarihmic growth phase for ChIP-assays
Growth protocol EBV positive B-cell (Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax
Extracted molecule genomic DNA
Extraction protocol ChIP-Seq protocol is as described previously (Lu et al, 2010 Virology journal 7, 262).
Library was constructed using the TruSeq ChIP Sample Prep kit (Illumina) according to manufacturers instructions
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description WST_LCL_H3K27me3
Data processing All chip-seq files were generated by Illumina GA II and base calling was done with CASAVA 1.5
Chip-seq files were aligned to human genome hg19 using bowtie using "-v 2 -m 1 -best -strata" option on unique reads
Peak calling was done with homer (v1.0) software
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output
 
Submission date Nov 30, 2015
Last update date May 15, 2019
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 GPL9115
Series (2)
GSE75503 Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2 [ChIP-seq]
GSE75504 Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2
Relations
BioSample SAMN04301882
SRA SRX1456201

Supplementary file Size Download File type/resource
GSM1958047_LCL_H3K4me3_vs_LCL_IgG.peak.txt.gz 559.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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