Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TCF7L2

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
chip antibody
TCF7L2 (Cell Signaling Technology C48H11, 2569)
passage
15
growth protocol
Cells were grown in RPMI with 10% FBS (not charcoal-stripped) and collected when 80% confluent

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
38601556
Reads aligned (%)
93.3
Duplicates removed (%)
4.6
Number of peaks
13828 (qval < 1E-05)

hg38

Number of total reads
38601556
Reads aligned (%)
95.6
Duplicates removed (%)
3.1
Number of peaks
13664 (qval < 1E-05)

Base call quality data from DBCLS SRA