Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD3

Cell type

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

Attributes by original data submitter

Sample

source_name
H1 human Embryonic stem cells (hESC)
cell line
H1
cell type
H1 hESC
state
RPMI+ B27 media for 24hrs and 50 ng/ml Activin for 48 hrs
antibody
SMAD3, Abcam, AB28379

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, cells were crosslinked with 1% formaldehyde for 10 minutes prior to sonication to solubulize the chromatin. The sheared chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibody against SMAD3. Purified immunoprecipitated DNA samples were prepared for sequencing using the Truseq ChIP kit from Illunima.  ChIP-seq libraries were prepared according to instructions accompanying the TruSeq ChIP Kit and barcoded for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
46703745
Reads aligned (%)
74.5
Duplicates removed (%)
21.4
Number of peaks
1912 (qval < 1E-05)

hg38

Number of total reads
46703745
Reads aligned (%)
75.9
Duplicates removed (%)
20.4
Number of peaks
1954 (qval < 1E-05)

Base call quality data from DBCLS SRA