title: shCtrl_ATACseq_replicate1
organism: Homo sapiens
description: Protocols: Chromatin accessibility mapping was performed using the ATAC-seq method as described in (Corces, M.R. et al., An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues., Nat Methods, 2017). For the transposition reaction cell nuclei were carefully resuspended in (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30min at 37°C on a shaker at 1000rpm. MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC) and cultured under standard conditions in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1.0µg/ml puromycin. Stably transduced MDA-MB-231 shCtrl and shZEB1 cell lines were generated as described in (Spaderna, S. et al., The transcriptional repressor ZEB1 promotes metastasis and loss of cell polarity in cancer., Cancer research, 2008). DNA was purified with the Clean and Concentrator-5 kit (Zymo). Library material was amplified using custom Nextera primers and was followed by SPRI size selection with AmpureXP beads to exclude most fragments larger than 1,200bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-07-22T08:04:40Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-08-20T15:27:55Z
attributes.tag: External Id
attributes.value: SAMEA5877039
attributes.tag: INSDC center name
attributes.value: Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany
attributes.tag: INSDC first public
attributes.value: 2020-07-22T08:04:40Z
attributes.tag: INSDC last update
attributes.value: 2019-08-20T15:27:55Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8264:shCtrl_ATACseq_replicate1
attributes.tag: age
attributes.value: 51
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: MDAMB231
attributes.tag: cell type
attributes.value: mammary epithelial cell
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: breast adenocarcinoma
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: mammary gland
attributes.tag: sample name
attributes.value: E-MTAB-8264:shCtrl_ATACseq_replicate1
attributes.tag: scientific_name
attributes.value: Homo sapiens