Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
mouse embryionic stem cells
cell type
Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells
treatment
DMSO
passage
p9
chip ab / kit
H3K27me3 (Diagenode, C15410195, lot A1811-001P)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
formaldehyde fixed chromatin was preprocessed following RELACS high-thoughput ChIP-seq protocol (Arrigoni et al., 2019) using Covaris sonicator. For end repair, a-tailing, barcoding, and adaptor ligation we use reagents from the NEBNext Ultra II kit. RNA was extracted using RNeasy Mini Kit and processed using TrueSeq Stranded mRNA kit. ATAC-seq was generated following the protocol of Buerostro et al. 2015. Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After illumina adapter ligation, library was PCR amplified (15 cycles). Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq3000 (RELACS ChIP-Seq, ATAC-Seq) and NextSeq HIGH (RNA-Seq) following manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
71813853
Reads aligned (%)
92.1
Duplicates removed (%)
55.6
Number of peaks
65 (qval < 1E-05)

mm9

Number of total reads
71813853
Reads aligned (%)
92.0
Duplicates removed (%)
55.7
Number of peaks
49 (qval < 1E-05)

Base call quality data from DBCLS SRA