Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX9

Cell type

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

Attributes by original data submitter

Sample

source_name
Pancreatic progenitor cells
cell line
CyT49
source cell type
human embryonic stem cells
cell type
hESC-derived pancreatic progenitor cells
chip antibody
SOX9
chip antibody vendor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitations were performed as previously described (Bhandare et al., 2010). Briefly, samples were crosslinked in 1.1% formaldehyde/PBS for 15 min at room temperature and then quenched with 0.125M glycine/PBS. Samples were subsequently washed twice with PBS and then lysed in 1% SDS. For sonication, lysates were sonicated with a Bioruptor Sonicator (Diagenode) six times for 5 min each with a 30 sec on and off cycle, resulting in 200-500bp chromatin fragments. Sheared chromatin was incubated overnight at 4 °C with 5 µg rabbit anti-SOX9 antibody (Millipore, AB5535; Lot number 2262679). Chromatin and antibody complex was incubated with 12.5 µl of Dynabeads protein A plus 12.5 µl of Dynabeads protein G (Life Technologies) at 4 °C for 4 hrs. Immunoprecipitated complexes were further eluted, reverse crosslinked, and subjected to library preparation. ChIP-seq libraries were prepared as per Illumina’s instructions (http://www.illumina.com). For input library preparation, 50 ng of input DNA from each sample was used. After adaptor ligation, DNA fragments were size-fractionated by gel electrophoresis and excised at 200±25 bp. Following gel purification, DNA fragments were amplified with 18 PCR cycles and purified using a MiniElute PCR Purification kit (Qiagen). 10 nM purified DNA was loaded on the flow cell, and sequencing was performed on an Illumina/Solexa Genome Analyzer II in accordance with the manufacturer’s protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
248229382
Reads aligned (%)
55.7
Duplicates removed (%)
43.2
Number of peaks
2542 (qval < 1E-05)

hg38

Number of total reads
248229382
Reads aligned (%)
57.7
Duplicates removed (%)
41.7
Number of peaks
3274 (qval < 1E-05)

Base call quality data from DBCLS SRA