Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

Cell type Class
Blood
Cell type
TF-1
Primary Tissue
Blood
Tissue Diagnosis
Erythroleukemia

Attributes by original data submitter

Sample

source_name
TF-1-RAD21 Q592* (SMC3 #1)
cell line
TF-1
cell type
Erythroleukemia Cell Line
transduction
TF-1-RAD21 Q592* (SMC3 #1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
~100,000,000 cells were were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Typically, 5 million cells were used for each ChIP experiment and chromatin was sheared on a Bioruptor (Diagenode) to an average of 200-400bp. The following antibodies were used for ChIP studies: SMC3 (clone: ab9263, Abcam), GATA2 (Clone: sc-9008, Santa Cruz Biotechnology) and RUNX1 (Clone: sc-365644, Santa Cruz Biotechnology) After specific recovery of chromatin bound proteins via immunoprecipitation, samples were reverse crosslinked at 65°C overnight and DNA was purified for subsequent library preparation. ChIP-seq libraries were prepared according to the NEBNext protocol and sequenced using Illumina NextSeq.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
58948669
Reads aligned (%)
84.1
Duplicates removed (%)
13.8
Number of peaks
1073 (qval < 1E-05)

hg38

Number of total reads
58948669
Reads aligned (%)
85.6
Duplicates removed (%)
12.8
Number of peaks
1301 (qval < 1E-05)

Base call quality data from DBCLS SRA