Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NCAPH2

Cell type

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

Attributes by original data submitter

Sample

source_name
Human embryonic kidney cells 293
cell line
HEK293
cell type
human embryonic kidney cells
passages
10-13 passages
antibody
NCAPH2 (Bethyl: A302-275A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Standard ChIP protocol was used. Briefly, nuclei were isolated using nuclearlysis buffer, followed by being lysed with SDS buffer to extract chromatin. The chromatin was sheared by Covaris sonicator to a size range of 300-700 base pairs. The chromatin samples were incubated with 6 μL antibodies overnight at 4°C with rotation, followed by incubation with Protein A/G dynabeads for 2 hours at 4°C with rotation. . The beads were washed twice with 0.1% SDS Lysis Buffer for 5 min each at 4°C, followed by washing twice with High Salt Wash Buffer for 5 min each at 4°C, followed by washing twice with Lithium Chloride Wash Buffer for 5 min each at 4°C. After that, the beads were washed with TE buffer with 0.2% Triton. Chromatin was eluted by adding elution buffer. Eluted chromatin was reverse cross-linked by adding 0.3M NaCl and incubating it overnight at 65°C, which is followed by treatment of 6 μL proteinase K. Chromatin was purified by Qiagen PCR purification kit (Qiagen, 28106), following the manufacturer's protocol. The Illumina adaptors were added to each chromatin sample for Solexa sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
18974410
Reads aligned (%)
96.0
Duplicates removed (%)
2.3
Number of peaks
470 (qval < 1E-05)

hg38

Number of total reads
18974410
Reads aligned (%)
96.7
Duplicates removed (%)
2.0
Number of peaks
256 (qval < 1E-05)

Base call quality data from DBCLS SRA