Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3

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
C57BL/6
antibody
anti-H3 (ab1791)
ChIP
crosslink
genotype/variation
H3.3B-KO

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
288254216
Reads aligned (%)
82.4
Duplicates removed (%)
13.2
Number of peaks
1304 (qval < 1E-05)

mm9

Number of total reads
288254216
Reads aligned (%)
82.2
Duplicates removed (%)
13.1
Number of peaks
1529 (qval < 1E-05)

Base call quality data from DBCLS SRA