Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TET2

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
prostate cancer cells
cell line
LNCaP
cell type
prostate cancer
treatment
no treatment
chip antibody
TET2 (abcam ab94580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. For 5-mC and 5-hmC immunoprecipitation, we used methycollector and hydroxymethylcollector (Active motif) to obtain double stranded DNA modified with 5-mC and 5-hmC. The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN). 300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
33189879
Reads aligned (%)
53.6
Duplicates removed (%)
43.2
Number of peaks
973 (qval < 1E-05)

hg38

Number of total reads
33189879
Reads aligned (%)
56.0
Duplicates removed (%)
41.3
Number of peaks
814 (qval < 1E-05)

Base call quality data from DBCLS SRA