Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TET3

Cell type

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

Attributes by original data submitter

Sample

source_name
HEK 293T cells
antibody
TET3
cell line
HEK 293T

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
293T cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication. DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles. Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp were isolated from agarose gel.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
32943612
Reads aligned (%)
3.6
Duplicates removed (%)
95.2
Number of peaks
329 (qval < 1E-05)

hg38

Number of total reads
32943612
Reads aligned (%)
4.0
Duplicates removed (%)
94.7
Number of peaks
317 (qval < 1E-05)

Base call quality data from DBCLS SRA