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
ES cell culture
strain
V6.5
cell type
mouse embryonic stem cell
antibody
none
transfection
shMLL2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106). ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions. 2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Pre Kit (Illumina #RS-122-2001).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14410163
Reads aligned (%)
97.7
Duplicates removed (%)
17.1
Number of peaks
408 (qval < 1E-05)

mm9

Number of total reads
14410163
Reads aligned (%)
97.4
Duplicates removed (%)
17.2
Number of peaks
407 (qval < 1E-05)

Base call quality data from DBCLS SRA