Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RBPJ

Cell type

Cell type Class
Breast
Cell type
HCC1599
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
HCC1599 cell line
cell line
HCC1599
cell type
Triple-negative breast cancer cell line
chip antibody
RBPJ
drug treatment
GSI-washout

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (107 for histone modifications and 4 x 107 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106). Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
69724032
Reads aligned (%)
185.9
Duplicates removed (%)
3.6
Number of peaks
26745 (qval < 1E-05)

hg38

Number of total reads
69724032
Reads aligned (%)
188.7
Duplicates removed (%)
3.1
Number of peaks
27388 (qval < 1E-05)

Base call quality data from DBCLS SRA