characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-03-30T12:17:29Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-03-30T12:17:29Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112642682
characteristics.characteristic: External Id
characteristics.text: UZH
characteristics.characteristic: INSDC center name
characteristics.text: 2023-03-30T12:17:29Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-03-30T12:17:29Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14634651
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12612:Sample 66
characteristics.characteristic: Submitter Id
characteristics.text: 72
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: R
characteristics.characteristic: colon segment
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: This validation study was performed on 41 cADNs, 18 SSLs, and their adjacent normal mucosa samples (total number of samples analyzed = 118). Colorectal tissues were prospectively collected during colonoscopies. Endoscopic biopsies from the tumor and the corresponding normal mucosa (located >2 cm from the tumor) were immersed in AllProtect Tissue Reagent (Qiagen, Hilden, Germany), held at 4°C overnight, and stored at -80°C. onors provided written consent to tissue collection, testing and data publications. Samples were numerically coded to protect donors' rights to confidentiality and privacy. The study was approved by the Zurich canton ethics committee. DNA extraction was performed with Qiagen AllPrep DNA/RNA mini kit (Hilden, Germany). DNA concentrations were quantified using Qubit fluorometer (Invitrogen, Carlsbad, USA) and quality was assessed with NanoDrop (ThermoFisher Scientific, Wilmington, USA). Genomic DNA (100ng) was bisulfite converted with EZ-DNA Methylation-Gold kit (Zymo, Irvine, USA) prior to library preparation which was performed with Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences, Ann Arbor, USA). Eight indexed libraries were pooled in equimolar amounts for hybridization with baits. Hybridization of customized RNA baits with the pool of 8 libraries was performed twice at 63°C for 16 to 24 hours. AMPure Xp beads (Beckman Coulter Inc, Brea, USA) were used to isolate biotinylated DNA, and amplification of bead-bound enriched libraries was performed using the KAPA HiFi HotStart Ready Mix (KAPA Biosystems, Wilmington, MA, USA) and adaptor specific primers. The concentration of the enriched libraries was determined with a Qubit fluorometer, and library size with a Tapestation (Agilent, Santa Clara, CA, USA) for subsequent library titration and next generation sequencing.
characteristics.characteristic: description
characteristics.text: adenoma
characteristics.characteristic: disease
characteristics.text: A33
characteristics.characteristic: individual
characteristics.text: normal
characteristics.characteristic: microscopic appearance
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: colon
characteristics.characteristic: organism part
characteristics.text: normal
characteristics.characteristic: paris classification
characteristics.text: normal
characteristics.characteristic: pit pattern classification
characteristics.text: normal tissue adjacent to pre-lesion (>2cm)
characteristics.characteristic: sampling site
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 01/10/21
characteristics.characteristic: sequencing date
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: Sample 66
characteristics.characteristic: title