Homo sapiens
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.
ENA-FIRST-PUBLIC
2023-03-30
ENA-LAST-UPDATE
2023-03-30
External Id
SAMEA112642642
INSDC center alias
UZH
INSDC center name
University of Zurich
INSDC first public
2023-03-30T12:17:29Z
INSDC last update
2023-03-30T12:17:29Z
INSDC status
public
Submitter Id
E-MTAB-12612:Sample 3
age
68
broker name
ArrayExpress
colon segment
A
common name
human
disease
adenoma
dysplasia
LGD
individual
A2
maximum lesion diameter
35
microscopic appearance
TA
number of lesions at study colonoscopy
1
organism part
colon
paris classification
ISP
pit pattern classification
IV
sample name
E-MTAB-12612:Sample 3
sampling site
pre-lesion
scientific_name
Homo sapiens
sequencing date
13/12/20
sex
male