Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZBTB7A

Cell type

Cell type Class
Blood
Cell type
HUDEP-2
NA
NA

Attributes by original data submitter

Sample

source_name
HUDEP2 (ΔGγ) WT ZBTB7A ChIP-seq
cell line
HUDEP-2
antibody
ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP experiments were performed as previously described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using highthroughput sequencing to discover protein-DNA interactions. Methods. Jul 2009;48(3):240-248). Briefly, approximately 5x107-1x108 cells were used for each IP. Cells were crosslinked with 1 % formaldehyde for 10-15 min at RT and the reaction was quenched with glycine at a final concentration of 125 mM. Crosslinked cells were then lysed and sonicated to obtain ~200–300 bp fragments of chromatin. Crosslinked DNA was pulled down at 4 °C overnight using antibody against V5-tag (R960CUS, Life Technologies), ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82) or control anti-goat IgG (sc-2028). Chromatin was then reverse crosslinked and eluted at 65°C overnight and DNA was purified.If ChIP material was subjected to sequencing, DNA was purified using a Qiagen MinElute Reaction Clean-up kit. Standard Illumina TruSeq

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
52150161
Reads aligned (%)
36.4
Duplicates removed (%)
62.0
Number of peaks
27535 (qval < 1E-05)

hg38

Number of total reads
52150161
Reads aligned (%)
37.2
Duplicates removed (%)
61.4
Number of peaks
27598 (qval < 1E-05)

Base call quality data from DBCLS SRA