Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDKN1B

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
colon cancer cells
cell line
colon cancer cell line HCT116
cell growth
G0 synchronized
chip antibody
p27 (Santa Cruz, catalog# sc-528, lot# I 2115)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and chromatine-DNA complexes were isolated with anti-p27 and anti-PCAF antibodies Libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of "A" bases to 3' ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 5092816 and 50928006). Library size selection was done with 2% low-range agarose gel. Library amplification was performed by PCR on the size selected fragments. final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior toamplification with Illumina's cBot. sequencing was done on the HiSeq2000, single Read, 50 nts

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24948727
Reads aligned (%)
91.1
Duplicates removed (%)
6.2
Number of peaks
1241 (qval < 1E-05)

hg38

Number of total reads
24948727
Reads aligned (%)
93.1
Duplicates removed (%)
4.9
Number of peaks
1123 (qval < 1E-05)

Base call quality data from DBCLS SRA