Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

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

Attributes by original data submitter

Sample

source_name
ESCs
cell type
ESCs
genotype/variation
RGd2_clone 6
growth
withdrawn from 2i for 25h, Rex1-high population
line
RGd2 clonal line 6
ChIP
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-DNA was eluted with Qiagen MinElute PCR purification kit Ev5-ChIP-Seq libraries were generated using NEB Next ChIP-Seq Library Prep Master Mix Set for Illumina (NEB. For H3K4me3 ChIP-seq libraries DNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (∼300 bp) and 14 cycles of PCR amplification. Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) platform according to standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
38699343
Reads aligned (%)
96.9
Duplicates removed (%)
22.0
Number of peaks
50141 (qval < 1E-05)

mm9

Number of total reads
38699343
Reads aligned (%)
96.8
Duplicates removed (%)
22.1
Number of peaks
50148 (qval < 1E-05)

Base call quality data from DBCLS SRA