characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2016-05-19T17:00:51Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T22:11:34Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3174173
characteristics.characteristic: External Id
characteristics.text: Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
characteristics.characteristic: INSDC center name
characteristics.text: 2016-05-19T17:00:51Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T22:11:34Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS627714
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-3160:HA_Rep2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: MCF-7
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001203
characteristics.characteristic: cell line
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: MCF-7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37°C incubator with 5% CO2. Immunoprecipitation was performed according to the manufacturer’s protocol (Upstate Biotechnology, Inc., Lake Placid, NY) with slight modifications. MCF-7 cells were fixed for 10 min with 1% of formaldehyde at room temperature, and then quenched with a final of 1M of glycine. The cells were lysed and the chromatin was sonicated to 200-500 bp fragments with a Bioruptor (Diagenode, Sparta, NJ). Chromatin was immunoprecipitated by using anti-HA tag antibody (ab1424; Abcam) and Protein A Agarose beads. The beads were washed once with each washing buffer, including low salt immune complex wash buffer, high salt immune complex wash buffer, and LiCl immune complex wash buffer, and twice with 1X TE buffer. Precipitates were eluted with 1% of SDS and 100 mM of NaHCO3. The samples were heated at 65°C for 6 hr in order to reverse cross-link, extracted with phenol/chloroform, ethanol-precipitated. The sequencing libraries were constructed from immunoprecipitated and input DNA using TruSeq ChIP Sample Preparation Kit (Illumina Inc., USA) according to the manufacturer’s instruction. The fragmented DNA was end repaired following by addition 3’-A to the ends and ligation of adapters. The adapter-ligated DNA library was sized-selected (300-500 bp) on a 2% agarose gel and amplified by PCR for 16 cycles with the use of KAPA HiFi DNA Polymerase (Kapa Biosystems).
characteristics.characteristic: description
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: HA_Rep2
characteristics.characteristic: title