Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic stem cells
strain
129/C57Bl/6
antibody
no antibody
ChIP
NA
cell line
ESC
genotype/variation
H3.3 KO1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
185452094
Reads aligned (%)
93.8
Duplicates removed (%)
7.7
Number of peaks
599 (qval < 1E-05)

mm9

Number of total reads
185452094
Reads aligned (%)
93.7
Duplicates removed (%)
8.2
Number of peaks
637 (qval < 1E-05)

Base call quality data from DBCLS SRA