Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic stem cells
cell line
H1
cell type
human embryonic stem cells (hESCs)
treatment
untreated
treatment_duration_mins
0
chip antibody
smad1 (Cell Signaling Technology; CST6944)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were dissociated and fixed in mTeSR1 media with formaldehyde at a final concentration of 1% for 10 minutes. Fixation was quenched with glycine and cells were washed with DPBS. Cells were suspended in high salt lysis buffer and chromatin was sheared using a Bioruptor Plus to sizes of 100-400 bp. Soluble chromatin from approximately 3E+06 cells per ChIP was incubated with primary antibody (Cell Signaling Technology; CST6944) and Protein G Dynabeads at 4 degrees overnight. Dynabeads were then washed and bound chromatin was eluted. Crosslinks were reversed by incubation at 65 degrees overnight, and proteins were digested with Proteinase K. DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit. 2 ng of DNA was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer recommendations (15 cycles of PCR). Library quality and quantity were assessed on a Bioanalyser and Qubit respectively.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
128617949
Reads aligned (%)
62.1
Duplicates removed (%)
35.0
Number of peaks
2178 (qval < 1E-05)

hg38

Number of total reads
128617949
Reads aligned (%)
63.5
Duplicates removed (%)
33.9
Number of peaks
2466 (qval < 1E-05)

Base call quality data from DBCLS SRA