Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sp3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
A17Lox_ESC
cell type
ESC
cell line
A17Lox
chip antibody
Sp3 (Santa Cruz sc644X)
genotype
Sp1KO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested and washed with PBS prior to a 2-step crosslinking procedure. Proteins were crosslinked by incubating cells for 45min at RT in PBS supplemented with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG, Sigma). Cells were then washed 4 times with PBS, prior to formaldehyde crosslinking of proteins and DNA for 10min at RT using 1% formaldehyde (Pierce) in IMDM with 10% FCS. Formaldehyde was quenched by adding 1/10th volume 2M glycine and crosslinked cells were washed twice in ice-cold PBS. Single crosslinked samples were treated with 1% formaldehyde crosslinking only. Nuclei were prepared essentially as described in Lefevre et al 2003. Antibody incubated with chromatin 2-4hrs at 4 degrees. Kapa Hyper-prep kit

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
32364500
Reads aligned (%)
96.0
Duplicates removed (%)
21.2
Number of peaks
26565 (qval < 1E-05)

mm9

Number of total reads
32364500
Reads aligned (%)
95.8
Duplicates removed (%)
21.2
Number of peaks
26468 (qval < 1E-05)

Base call quality data from DBCLS SRA