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
mouse embryonic stem cell
cell type
Embryonic stem cells
treatment
UNC4219 (control compound)
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP samples were prepared as previously reported (Moussa et al., Nature Communications 2019, doi:10.1038/s41467-019-09628-6). For Capture ChIP-seq, 120nt-long MYbaits sequence capture probes (Arbor Biosciences) were custom designed for 24 genomic loci based on mm9 genome build. Designed probes were tiled at an approximate density of 1.26 (=starting approx. every 95bp) to cover a total of 1,960,734 bp. After repeat masking, candidate probes were filtered for stringent specificity. Sequence capture from genomic DNA recovered in ChIP was carried out according to manufacturer's instructions. Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol and doubling the incubation times for all enzymatic steps. Each sample of ChIPed DNA was end-repaired and ligated to unique barcoded adaptors to produce individual libraries. Libraries corresponding to samples to be directly compared to each other (e.g. +IAA vs -IAA) were pooled together and purified using 1 volume of Agencourt AMPure XP (Beckman Coulter). The pooled libraries were eluted with 25 µL of elution buffer (NEXTflex ChIP-Seq kit) and amplified using the KAPA Real-Time Library Amplification Kit (peqlab) following the kit instructions. Finally, the amplified libraries were size-selected to fragments of 200-800 bp by running them on 1.5% agarose gel, and staining with 1x SYBR Gold (Thermo Fisher) to visualize the DNA on a blue light LED screen and cut the appropriate fragments. The size selected libraries were gel purified with the Monarch DNA Gel extraction kit (NEB).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
294819
Reads aligned (%)
93.5
Duplicates removed (%)
8.0
Number of peaks
7 (qval < 1E-05)

mm9

Number of total reads
294819
Reads aligned (%)
93.4
Duplicates removed (%)
8.0
Number of peaks
7 (qval < 1E-05)

Base call quality data from DBCLS SRA