Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PDX1

Cell type

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

Attributes by original data submitter

Sample

source_name
hESCs differentiated into pancreatic lineage
age
day 17
cell type
hESCs differentiated into pancreatic lineage
antibody
PDX1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Two 6-well transwell plates of day 17 differentiated hESCs were sonicated for 2 min x 90 % pulse x 5 times using Ultrasonic 3000 Ultrasonic homogenizer (Biologics, Inc). For ChIP-seq, libraries were prepared using the Solexa ChIP-seq DNA Sample Prep Kit (IP102-1001). After amplification, DNA fragments between 180 and 400 bp were gel extracted and sent for sequencing. Libraries were sequenced by the Genome Institute of Singapore using the Illumina Genome Analyzer II as single-end 35 bp reads

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
16127244
Reads aligned (%)
91.9
Duplicates removed (%)
4.2
Number of peaks
5344 (qval < 1E-05)

hg38

Number of total reads
16127244
Reads aligned (%)
93.7
Duplicates removed (%)
3.4
Number of peaks
5238 (qval < 1E-05)

Base call quality data from DBCLS SRA