shCtrl_ATACseq_replicate1
Homo sapiens
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).
ENA-FIRST-PUBLIC
2020-07-22T08:04:40Z
ENA-LAST-UPDATE
2019-08-20T15:27:55Z
External Id
SAMEA5877039
INSDC center name
Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany
INSDC first public
2020-07-22T08:04:40Z
INSDC last update
2019-08-20T15:27:55Z
INSDC status
public
Submitter Id
E-MTAB-8264:shCtrl_ATACseq_replicate1
age
51
broker name
ArrayExpress
cell line
MDAMB231
cell type
mammary epithelial cell
common name
human
developmental stage
adult
disease
breast adenocarcinoma
genotype
wild type genotype
organism part
mammary gland
sample name
E-MTAB-8264:shCtrl_ATACseq_replicate1
scientific_name
Homo sapiens