characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-06-01T16:20:34Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T22:09:12Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3175638
characteristics.characteristic: External Id
characteristics.text: Institute for molecular and tumor biology Philipps University Marburg Germany
characteristics.characteristic: INSDC center name
characteristics.text: 2015-06-01T16:20:34Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T22:09:12Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS628586
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-3166:TA017
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: tumor associated macrophage
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Ascites was collected from 30 patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committe After Ficoll gradient purification, cells were incubated in Greiner flasks in autologous ascites for 1 h at 37 degrees C in a humidified incubator with 5% CO2 (adherence selection). Nonadherent cells were removed by two PBS washing steps. Using a final concentration of 1% (w/v) formaldehyde for ten minutes at room temperature, proteins and DNA were crosslinked. After adding glycine to a final concentration of 125 mM, the cells were washed twice with ice-cold PBS. After harvesting by scraping and centrifugation, the pellet was resuspended in 1 ml hypotonic ChIP lysis buffer per 8x10^6 cells with protease inhibitors (Sigma) and incubated for 20 minutes. After centrifugation, nuclei were resuspended in ChIP lysis buffer II (RIPA) containing protease inhibitors and sheared with a Branson S250D using a microtip (52 pulses of 1 s, 2 s pause, 20% amplitude) with coolling (ice-ethanol). A 15 min 20,000xg supernatant was used for IP (after preclearing). ChIP was performed as in Adhikary and Mueller, Peroxisome Proliferator-Activated Receptors (PPARs) Methods in Molecular Biology Volume 952, 2013, pp 175-185. DNA was purified using Qiagen Minelute columns. Preceding the PE washing step, the membranes were washed twice with pure methanol in order to remove contaminating DNA-binding lipids that inhibit subsequent low-temperature enzymatic modification steps, which we found to be present in samples from primary macrophages. Libraries were synthesized from 1-2 ng of genomic DNA using the MicroPlex kit (Diagenode, Seraing, Belgium).
characteristics.characteristic: description
characteristics.text: OC52TAM
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0003237
characteristics.characteristic: individual
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: TA017
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005309
characteristics.characteristic: title