Illumina HiSeq 2500 paired end sequencing; The ETS transcription factor ELF5 modulates estrogen action in breast cancer via participation in FOXA1-ER driven transcription.
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
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
ENA first public
2020-01-06
ENA last update
2019-01-31
ENA-CHECKLIST
ERC000011
External Id
SAMEA5313143
INSDC center alias
Garvan Institute of Medical Research and The Kinghorn Cancer Centre
INSDC center name
Garvan Institute of Medical Research and The Kinghorn Cancer Centre
INSDC first public
2020-01-06T04:04:24Z
INSDC last update
2019-01-31T16:19:09Z
INSDC status
public
Submitter Id
E-MTAB-7641:ERDox2
broker name
ArrayExpress
cell line
MCF-7
cell type
BTO:0000093
common name
human
developmental stage
Cancer cell line
disease
breast carcinoma
genotype
MCF7-ELF5-Isoform2-V5
organism part
breast
replicate
2
sample name
E-MTAB-7641:ERDox2
stimulus
Doxycyclin
Sequenced DNA Library
library_name
ERDox2_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ELF5 Isoform 2 cell lines were created and maintained as described in Kalyuga et al. 2012. Cells were fixed in 1% formaldehyde, at 37°C for 10 min, washed 2× with cold PBS, scraped into 600 µl PBS with protease inhibitors (P8340, Sigma), spun 2 min at 6,000 g, washed as before, and snap frozen in liquid nitrogen. Puromycin (Sigma-Aldrich, St Louis, Missouri, USA) at 1ug/mL was used to maintain selection. Doxycycline (Dox, Sigma-Aldrich) at 0.1ug/mL in water was used daily to induce ELF5. Four independent replicates for ER, FOXA1, ELF5-V5 and H3K4me3 ChIP-seq were performed according to the protocols described in published in “Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer” by Holmes, Brown and Carroll 2016 (https://link.springer.com/protocol/10.1007%2F978-1-4939-3127-9_8), and our previous publications in Hurtado et al. 2011 and Kalyuga et al. 2012. DNA purification following IP was performed using phenol:chloroform:isoamyl alcohol and Phase Lock Gel tubes. Libraries were prepared using the TruSeq ChIP Sample Preparation Kit (A) from Illumina, with AMPure XP bead double-sided size selection.