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Sample GSM1359506 Query DataSets for GSM1359506
Status Public on Apr 01, 2014
Title ChIPseq_PolII_iSLK219
Sample type SRA
 
Source name Kidney epithelium
Organism Homo sapiens
Characteristics cell type: Kidney epithelial cells
infection: rKSHV.219
cell line: iSLK-219
chip antibody: Pol II (Santa Cruz Biotechnology, sc-899 X)
Treatment protocol When indicated, 1 µM doxycyclin (dox) and 500 µM phosphonoformic acid (PFA) were added to the culture medium for 72 hrs
Extracted molecule genomic DNA
Extraction protocol 1 x 10^7 cells were fixed with 1% formaldehyde 5 minutes prior to harvest. Nuclei preparations were done using the truChIP High Cell Chromatin Shearing Kit with SDS from Covaris and chromatin was sheared with a Covaris E220 Ultrasonicator. The average size of chromatin fragments was ~200 bp. Antibodies for ChIP were coupled to Dynabeads (Invitrogen) and incubated with chromatin extracts for 4 hours at 4C in cold RIPA buffer (10 mM Tris pH 8.0, 1 mM EDTA, 150 mM NaCl, 5% glycerol, 0.1% Na deoxycholate, 0.1% SDS, 1% Triton X-100, protease inhibitors (Complete Mini, Roche)). Antibodies used for ChIP: rat α-LANA (Advanced Biotechnologies, 13-210-100), α-H3K4me3 (Abcam, ab8580), α-H3K27me3 (Millipore, 07-449), α-H3K36me3 (Abcam, ab9050), and α-Pol II (Santa Cruz Biotechnology, sc-899 X). The immunoprecipitated chromatin was sequentially washed in high salt RIPA buffer (500 mM NaCl) and LiCl wash buffer (50 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 0.5% Na deoxycholate). Chromatin crosslinks were reversed by incubating samples overnight at 65°C in the presence of proteinase K (200 µg/ml, Invitrogen). DNA was recovered using AMPure XP beads (Beckman Coulter, Inc).
Libraries were prepared according to Illumina's instructions (TruSeq ChIP Sample Prep Kit, part # 15034288)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing Basecalls performed using CASAVA version 1.8
ChIPseq: reads were aligned to the hg19 genome assembly using Bowtie2 (v2.1.0, default parameters)
ChIPseq: peaks were called using MACS 1.4.2 using the default parameters except when otherwise specified (see Samples section)
RNAseq: reads were aligned to the hg19 genome assembly using TopHat2 (v2.0.8b, default parameters)
RNAseq: gene expression analysis was performed with the Cufflinks/Cuffdiff package v2.1.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq: peak calling output files from the MACS program (tab-delimited text format). Contain peak genomic location, tag abundance and peak score (p-value, FDR)
Supplementary_files_format_and_content: RNAseq: output files from Cufflinks and Cuffdiff (tab-delimited format) that include FPKM values, gene expression ratios (LEC219 vs LEC) and statistical analysis (scores) for all hg19-annotated genes
 
Submission date Mar 28, 2014
Last update date Apr 01, 2014
Contact name ALEXANDRE MERCIER
Organization name NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH
Department INFECTIOUS DISEASES
Lab DON GANEM
Street address 5300 CHIRON WAY
City EMERYVILLE
State/province CA
ZIP/Postal code 94608
Country USA
 
Platform ID GPL9115
Series (1)
GSE56144 Site-Specific Association with Host and Viral Chromatin by KSHV LANA and its Reversal during Lytic Reactivation
Relations
BioSample SAMN02711816

Supplementary file Size Download File type/resource
GSM1359506_ChIPseq_PolII_iSLK219_hg19.bed.gz 209.5 Mb (ftp)(http) BED
Processed data provided as supplementary file
Raw data not provided for this record

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