Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Placenta
Cell type
Trophoblast stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
Trophoblast stem cell
cell type
TSCs
genotype type
Esrrb overexpression
chip antibody
anti-H3K4me1 (Abcam, Ab8896)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
~10^5 cells were resuspended in lysis buffer and chromatin was sonicated to 200-500 bp with Covaris M220 system. Then, the sonicated chromatin was immunoprecipitated with the antibodies. Antibodies used in ChIP assays were Esrrb, H3k4me1, H3k4me2, H3k4me3 and H3k27ac. ChIP DNA was reverse-crosslinked, eluted, and purified by phenol-chloroform-isoamyl alcohol extraction, followed by ethanol precipitation. For sequencing, 10–100 ng DNA was used for library preparation following the New England Biolabs library preparation protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
14574942
Reads aligned (%)
94.8
Duplicates removed (%)
5.0
Number of peaks
47591 (qval < 1E-05)

mm9

Number of total reads
14574942
Reads aligned (%)
94.7
Duplicates removed (%)
5.0
Number of peaks
47569 (qval < 1E-05)

Base call quality data from DBCLS SRA