Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SRF

Cell type

Cell type Class
Blood
Cell type
HEL
Primary Tissue
Blood
Tissue Diagnosis
Erythroleukemia

Attributes by original data submitter

Sample

source_name
HEL-iMKL1 cells
treatment
Treated with 10ng/ml Dox for 24 hours
mkl overexpression
Overexpressed
tpa treatment
No TPA
ChIP
SRF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were first fixed in 1% formaldehyde with shaking for 10 minutes at room temperature. After PBS wash, they were sonicated at 4degrees Celsius in a BioRuptor, to obtain 200-300bp fragment sizes. They were pre-cleaned by incubating with Millipore Protein A Salmon-Sperm DNA coated beads, with shaking for 1 hour at 4degrees Celsius. Fixed chromatin was then incubated overnight with either anti-SRF or anti-IgG antibody, followed by 1-hour incubation with coated beads the following morning. DNA was eluted from the beads using high to low salt solutions, with the final elute in freshly made Tris-EDTA (TE) buffer. The DNA was then treated with Proteinase K and reverse cross-linked with 5M NaCl, before being sent for sequencing. Single end DNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Stem Cell Center Genomics Core

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
37849184
Reads aligned (%)
87.8
Duplicates removed (%)
5.4
Number of peaks
3914 (qval < 1E-05)

hg38

Number of total reads
37849184
Reads aligned (%)
89.9
Duplicates removed (%)
4.1
Number of peaks
3897 (qval < 1E-05)

Base call quality data from DBCLS SRA