characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2019-02-22T17:02:20Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-14T12:20:21Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104693370
characteristics.characteristic: External Id
characteristics.text: Georgia State University, Department of Biology
characteristics.characteristic: INSDC center name
characteristics.text: 2019-02-22T17:02:20Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-14T12:20:21Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS2294753
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6603:Sample 88
characteristics.characteristic: Submitter Id
characteristics.text: 43
characteristics.unit: year
characteristics.characteristic: age at diagnosis
characteristics.text: 28
characteristics.unit: month
characteristics.characteristic: breast cancer-specific survival in months
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: 0.466
characteristics.characteristic: cell cycle traverse rate
characteristics.text: Low
characteristics.characteristic: cell cycle traverse rate breast cancer-specific survival
characteristics.text: Low
characteristics.characteristic: cell cycle traverse rate mean
characteristics.text: Death from breast cancer
characteristics.characteristic: censoring for breast cancer-specific survival
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Pre-marked tumor areas in n=132 formalin-fixed paraffin-embedded (FFPE) malignant resection samples obtained prior to treatment from triple-negative breast cancer patients were obtained from the Nottingham Primary Breast Carcinoma series, selected based on the presence of sufficient tissue quantity for the analysis. The FFPE samples were deparaffinized with xylene, after which RNA was extracted using the Omega Mag-Bind XP FFPE RNA isolation kit (Omega, M2595-01) and the KingFisher Flex magnetic particle separator (ThermoFisher). Integrity was evaluated using the Agilent 2200 TapeStation instrument (Agilent Technologies, Santa Clara, CA). First-strand cDNA synthesis using random hexamers and reverse transcriptase was performed on ~100 ng RNA (25°C for 10 min, 42°C for 15 min, and 70°C for 15 min). Second-strand synthesis and RNA sequencing libraries were prepared per the manufacturer’s instructions using the TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA). RNA templates were removed and a second replacement strand was created by incorporating dUTP to generate double-stranded cDNA. Clean up was performed using Mag-Bind RxnPure Plus magnetic beads (Omega Bio-tek, Norcross, GA). cDNA 3’ ends were adenylated, and indexing adaptors were ligated. DNA fragments with adapter molecules on both ends were enriched using PCR (15 cycles of 98°C for 10 sec, 60°C for 30 sec, and 72°C for 30 sec). The Agilent 2200 TapeStation and QuantiFluor dsDNA System (Promega, Madiosn, WI) were used for library qualification and quantitation, respectively. 200 ng of each DNA library was combined to create a 4-plex pool of libraries, which were then mixed with capture probes specific to regions of interest, followed by hybridization (18 cycles of 1 min incubation, starting at 94°C, and then lowering by 2°C/cycle). Probes hybridized to the target regions were captured using streptavidin-coated magnetic beads. Enriched libraries were eluted and subjected to a second hybridization, then they were amplified by 10 cycles of PCR (98°C for 10 sec, 60°C for 30 sec, and 72°C for 30 sec). RxnPure magnetic beads were then used for clean-up. Final libraries were validated with the Agilent High Sensitivity D1000 ScreenTape on an Agilent 2200 Tapestation instrument.
characteristics.characteristic: description
characteristics.text: triple-negative breast cancer
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005537
characteristics.characteristic: disease
characteristics.text: 55
characteristics.characteristic: individual
characteristics.text: 70
characteristics.characteristic: ki67 percentage
characteristics.text: 3
characteristics.characteristic: lymph node stage
characteristics.text: 3
characteristics.characteristic: mitosis from grade
characteristics.text: 32.62
characteristics.characteristic: mitotic index
characteristics.text: 3
characteristics.characteristic: nottingham grade
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: neoplasm
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000616
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: paraffin specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000950
characteristics.characteristic: specimen with known storage state
characteristics.text: Sample 88
characteristics.characteristic: title
characteristics.text: adjuvant CMF received
characteristics.characteristic: treatment
characteristics.text: 2
characteristics.characteristic: tumour size