Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KSHV LANA

Cell type

Cell type Class
Kidney
Cell type
iSLK
NA
NA

Attributes by original data submitter

Sample

source_name
Kidney epithelium
cell type
Kidney epithelial cells
infection
rKSHV.219
cell line
iSLK-219
chip antibody
LANA (Advanced Biotechnologies, 13-210-100)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
34737014
Reads aligned (%)
97.6
Duplicates removed (%)
36.4
Number of peaks
1199 (qval < 1E-05)

hg19

Number of total reads
34737014
Reads aligned (%)
96.7
Duplicates removed (%)
37.9
Number of peaks
1301 (qval < 1E-05)

Base call quality data from DBCLS SRA