Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived mesendodermal cells
NA
NA

Attributes by original data submitter

Sample

source_name
hESC derived anterior foregut (AFG)
cell type
hESC derived anterior foregut (AFG)
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For Chip-seq, Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Antibodies were eluted from beads and formaldehyde cross-linking was reversed overnight by mild heating (65 °C), and chromatin was sequentially treated with RNase and Proteinase K before final column purification. Illumina sequencing libraries were generated using the TruSeq ChIP Sample Preparation Kit (Illumina). Briefly, 10 ng of ChIP-enriched DNA was end-repaired, 3’ adenylated, ligated with Illumina adapters, and amplified through 15 cycles of PCR amplification with Phusion High Fidelity DNA polymerase (Finnzymes) with primers directed against the adapters.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
52995835
Reads aligned (%)
91.0
Duplicates removed (%)
2.4
Number of peaks
1349 (qval < 1E-05)

hg19

Number of total reads
52995835
Reads aligned (%)
90.2
Duplicates removed (%)
3.5
Number of peaks
1317 (qval < 1E-05)

Base call quality data from DBCLS SRA