Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7 (ATCC HTB-22)
general
luminal epithelial breast cancer line; ER+, PR+/-, HER2-
Sex
female
passages
7 to 13
sample type
WT
antibody
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
100 ug of sonicated chromatin was used for immunoprecipitation and 1 ug (1%) was used for the input control. Libraries for input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and Atailed DNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bio Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (75 bp, single end) was performed on an Illumina NextSeq 500 sequencer using a 75-bp sequencing kit (v2) (Illumina Inc., San Diego, CA, USA). Base calling used Illumina NextSeq Control Software (NCS) v2.0, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0. RNA was isolated using a Qiagen RNeasy mini kit (Cat # 74104). Paired-end mRNA libraries were then prepared. Libraries were prepared by the Van Andel Research Institute Genomics Core from 1 μg of material using the KAPA Stranded mRNAseq Kit (v4.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 250–300 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
247262472
Reads aligned (%)
84.6
Duplicates removed (%)
11.2
Number of peaks
50471 (qval < 1E-05)

hg38

Number of total reads
247262472
Reads aligned (%)
86.9
Duplicates removed (%)
9.6
Number of peaks
52328 (qval < 1E-05)

Base call quality data from DBCLS SRA