title: DMSO ChIP
organism: Homo sapiens
description: Protocols: CrizR1 human cells are derived from the parental NCI-H3122 (CVCL_5160) and are resistant to crizotinib. CrizR1 cells were grown in 10cm2 dishes to 80% confluence and treated with DMSO, 200nM alvocidib or 100nM THZ1 for 6 hrs. Afterwards, cells were cross-linked in 1% formaldehyde for 10 mins at room temperature. After washing with ice-cold PBS, cells were collected by scraping in ice-cold PBS supplemented with protease inhibitors and genomic DNA isolated as follows. The protocol by (Nelson et al., 2006; https://doi.org/10.1038/nprot.2006.27) was followed to isolate chromatin. Briefly, cell pellets were sonicated for 25 cycles, with a 30s on, 45s off protocol. Then the input was reversed crosslinked and analysed on a gel to confirm efficient sonication. Input was then incubated O/N with Protein G beads bound to 10ug of total RNA polymerase II antibody (Diagenode, #C15200004) per sample. The chromatin was washed and eluted as per the cited protocol. The quality of the DNA was assessed using 2100 Agilent Bioanalyzer. Then, purified chromatin was used as input to generate PCR-amplified libraries using the Diagenode Microplex kit according to the manufacturer's instructions.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-13T17:05:17Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-09-25T16:27:01Z
attributes.tag: External Id
attributes.value: SAMEA5975618
attributes.tag: INSDC center name
attributes.value: UNIVERSITY OF MANCHESTER
attributes.tag: INSDC first public
attributes.value: 2020-05-13T17:05:17Z
attributes.tag: INSDC last update
attributes.value: 2019-09-25T16:27:01Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8380:DMSO ChIP
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: CrizR1
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: lung adenocarcinoma
attributes.tag: organism part
attributes.value: lung
attributes.tag: parental cell line
attributes.value: NCI-H3122
attributes.tag: phenotype
attributes.value: resistant to crizotinib
attributes.tag: sample name
attributes.value: E-MTAB-8380:DMSO ChIP
attributes.tag: scientific_name
attributes.value: Homo sapiens