GSM4915982: NR4A1 BRx142 day260 ovary; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
NR4A1
Cell type
Cell type Class
Breast
Cell type
Breast cancer cells
NA
NA
Attributes by original data submitter
Sample
source_name
Breast cancer circulating tumor cells
patient id
BRx142
tissue
xenograft ovary metastasis
timepoint
day 260
cell type
breast cancer circulating tumor cells
gender
female
chip antibody
NR4A1 (Novus Biologicals; Cat#NB100-56745)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell lines cultured in vitro, or tumor xenograft-derived and FACS-sorted single cell suspension were washed with ice-cold PBS, and crosslinked with 1% formaldehyde (Sigma) for 10 minutes (for histone modifications and RNA pol II) or 15 minutes (for transcription factors) at room temperature and quenched with glycine. ChIP was performed using EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore) following the recommended protocol. Briefly, nuclei were isolated with cold nuclei isolation buffer and sheared with Covaris S2 instrument with an optimized program (Duty Cycle: 5%; Intensity: 4; Cycles/Burst: 200; treatment time: 360s) to yield an average fragment size of approximately 300 bp. Chromatin was incubated with Protein A/G Dynabeads (ThermoFisher) together with 5 μg ChIP-grade antibody overnight at 4°C with rotation. The beads were then collected and washed extensively with high- and low-salt buffers. DNA was de-crosslinked and purified through ethanol precipitation. Before immunoprecipitation with Dynabeads and antibody, 10% of chromatin was saved as input control. Immunoprecipitated DNA from ChIP experiment, together with input DNA were all subjected to end repair, dA-tailing and ligation of Illumina sequencing adapters according to the instructions from KAPA Hyper Prep Kits (Kapa Biosystems). After ligation, the final PCR amplification was performed with KAPA Hifi Hotstart Readymix (2x, Kapa Biosystems), Illumina universal primer and Illumina index primer. Barcoded libraries were pooled and sequenced on Illumina HiSeq X platform with 150 bp paired-end reads.