organism: Homo sapiens
description: Protocols: 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-01-06T04:04:24Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-01-31T16:19:10Z
attributes.tag: External Id
attributes.value: SAMEA5313166
attributes.tag: INSDC center name
attributes.value: Garvan Institute of Medical Research and The Kinghorn Cancer Centre
attributes.tag: INSDC first public
attributes.value: 2020-01-06T04:04:24Z
attributes.tag: INSDC last update
attributes.value: 2019-01-31T16:19:10Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7641:Pool2InputDox2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: MCF-7
attributes.tag: cell type
attributes.value: BTO:0000093
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: Cancer cell line
attributes.tag: disease
attributes.value: breast carcinoma
attributes.tag: genotype
attributes.value: MCF7-ELF5-Isoform2-V5
attributes.tag: organism part
attributes.value: breast
attributes.tag: replicate
attributes.value: 1
attributes.tag: sample name
attributes.value: E-MTAB-7641:Pool2InputDox2
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: stimulus
attributes.value: Doxycyclin