Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
LUHMES
Tissue
Mesencephalon

Attributes by original data submitter

Sample

source_name
LUHMES
infection
HSV-1 17syn+
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
TGs were homogenized, crosslinked in 1% formaldehyde, and the cell lysates were sonicated. The sheared chromatin was pre-cleared with salmon-sperm DNA-protein A-agarose beads prior to antibody incubation. An aliquot representing 1/5 of the total sample volume was removed as a sample input (I). Both bound and input fractions were treated with 5M NaCl, RNAse A and proteinase K and the DNA was finally purified using a Qiaquick PCR purification kit. Prior to Illumina library construction and hybridization capture-based target enrichment. Briefly, 8 PCR-cycle indexed libraries were pooled for selection using the SureSelect XT hs system with custom probes spanning the HSV-1 genome (Roche). Samples were subject to 4 additional PCR cycles and used for 100 base pair paired-end Illumina sequencing on the HiSeq platform. Kappa biosystems hyperprep

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
57127799
Reads aligned (%)
0.7
Duplicates removed (%)
15.9
Number of peaks
480 (qval < 1E-05)

hg19

Number of total reads
57127799
Reads aligned (%)
0.7
Duplicates removed (%)
16.2
Number of peaks
450 (qval < 1E-05)

Base call quality data from DBCLS SRA