Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PHF20L1

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231 cell
cell line
MDA-MB-231
genotype/variation
control
chip antibody
anti-PHF20L1 (Sigma-Aldrich, HPA028417, A8319)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 5 x 10^7 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against PHF20L1, EZH2, MTA1, H3K27me2, H3K27me3 or H3K27ac. The DNA was purified with a Qiagen PCR purification kit A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 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 HiSeq 2000

hg19

Number of total reads
22155168
Reads aligned (%)
63.3
Duplicates removed (%)
11.9
Number of peaks
485 (qval < 1E-05)

hg38

Number of total reads
22155168
Reads aligned (%)
64.7
Duplicates removed (%)
10.5
Number of peaks
343 (qval < 1E-05)

Base call quality data from DBCLS SRA