Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZMYND8

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Kidney
cell line
HEK293
chip antibody
ZMYND8(Bethyl Laboratory, A302-089A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP DNA was collected using the SimpleChIP™ Enzymatic Chromatin IP Kit (Cell Signaling Technology #9005), according to the manufacturer’s protocol. Briefly, HEK293 cells were collected from 15 cm plates and treated with 1 % formaldehyde (cross-linking) for 10 min and 125 mM Glycine for another 5 min (quenching) at room temperature. After washing three times with 1X PBS, cells were lysed in buffer A for 10 min on ice, then washed once in buffer B. Cells were re-suspended in buffer B, then treated with MNase (2000 gel units per 100 ml reaction) at 37 ˚C for 30 min, before the digestion was stopped by adding EDTA (10 μl 0.5 mM EDTA per 100 μl reaction). Chromatin extracts were harvested following complete lysis of nuclei by sonication. Libraries were constructed using Wafergen’s PrepX Complete ILMN 32i DNA Library Kit (cat number 400076) with an input of 5ng where available using the Apollo 324

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
50405204
Reads aligned (%)
185.3
Duplicates removed (%)
5.7
Number of peaks
3522 (qval < 1E-05)

hg38

Number of total reads
50405204
Reads aligned (%)
186.5
Duplicates removed (%)
5.5
Number of peaks
3476 (qval < 1E-05)

Base call quality data from DBCLS SRA