characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-10-22T17:03:04Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-03-01T11:02:48Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA102064918
characteristics.characteristic: External Id
characteristics.text: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University
characteristics.characteristic: INSDC center name
characteristics.text: 2018-10-22T17:03:04Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-03-01T11:02:48Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1574201
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5537:MCF7SP103
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: epithelial cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000066
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: MCF-7/SP10+ and MCF-7/C breast cancer cells were routinely cultured in a humidified 95% air/5% CO2 incubator at 37 °C in complete medium Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) 1.0 mM sodium pyruvate, 2mM L-glutamine and 100 IU/mL penicillin. The low metastatic MCF-7 (ERα positive) epithelial breast cancer cells were transfected with transduction ready lentiviral particles containing short hairpin RNA (shRNA) against ERα (MCF-7/SP10+) and with control shRNA lentiviral particles that encode a scrambled shRNA sequence (MCF-7/C) Total RNA was isolated from cells using NucleoSpin® RNA plus Kit (Macherey-Nagel). The amount of isolated RNA was quantified by measuring its absorbance at 260 nm. Total RNA for AmpliSeq analysis was extracted in 3 biological replicates and 3 technical replicates as described above. 50 ng of RNA were reverse transcribed to cDNA using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit Preparation protocol (Revision A.0, Thermo Fisher). The acquired cDNA was amplified using Ion AmpliSeq™ Transcriptome Human Gene Expression core panel (Thermo Fisher) and the primer sequences were then partially digested. Then, DNA adaptors (Ion P1 Adaptor and Ion Xpress™ Barcode Adaptor, Thermo Fisher) were ligated to the amplicons. Adaptor ligated amplicons were purified using the Agencourt® AMPure® XP reagent (Beckman Coulter) and eluted in amplification mix (Platinum® PCR SuperMix High Fidelity and Library Amplification Primer Mix, Thermo Fisher) and amplified. Size-selection and purification was conducted using Agencourt® AMPure® XP reagent (Beckman Coulter). The amplicons were quantified using the Fragment AnalyzerTM instrument (Advanced Analytical Technologies, INC.) with DNF-474 High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, INC.). Samples were then pooled, six or less per pool, followed by emulsion PCR on either the Ion OneTouch™ 2 System using the Ion PI™ Hi-Q™ OT2 Kit (Thermo Fisher), or on the Ion Chef™ System using the Ion PI Hi-Q Chef Kit (Thermo Fisher). The pooled samples were loaded on Ion PI™ v3 chips and sequenced on the Ion Proton™ System using the Ion PI™ Hi-Q Sequencing 200 Kit chemistry (200 bp read length, Thermo Fisher). Mean read length was 114 bp.
characteristics.characteristic: description
characteristics.text: breast adenocarcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000304
characteristics.characteristic: disease
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: estrogen receptor alpha negative
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: MCF7SP103
characteristics.characteristic: title