Homo sapiens
Protocols: Freshly collected tissues (32 precancerous lesions and matched normal mucosa samples) were processed to investigate both their methylome and transcriptome. Paris classification: This classification schema places polyps into visual categories ranging from Ip (pendunculated), Is (sessile), IIa (slightly raised) to III (excavated/ulcerated) reference: The Paris endoscopic classification of superficial neoplastic lesions: esophagus, stomach, and colon: November 30 to December 1, 2002.[No authors listed]. Gastrointest Endosc. 2003 Dec;58(6 Suppl):S3-43. For methylation analysis, 1µg DNA was used for library preparation according to the Roche SeqCapEpi CpGiant protocol (Roche, Rotkreutz, Switzerland; details in Supplementary Experimental Procedures). Specifically with this method, DNA libraries were bisulfite converted prior to capture with a pre-designed probe pool (Roche-NimbleGen, Madison, WI) to enrich the methylation analysis to 80.5Mb of the genome, covering ~2.7 x 106 CpG sites (intra- and intergenic CpG islands, and gene promoters were thoroughly covered by this method, while CpG shores, enhancers and gene bodies were not as thoroughly investigated).
ENA-FIRST-PUBLIC
2018-11-23T17:04:22Z
ENA-LAST-UPDATE
2018-06-27T15:33:27Z
External Id
SAMEA4766529
INSDC center name
UZH
INSDC first public
2018-11-23T17:04:22Z
INSDC last update
2018-06-27T15:33:27Z
INSDC status
public
Submitter Id
E-MTAB-6952:A2_normal
age
68
braf status
normal
broker name
ArrayExpress
common name
human
disease
adenoma
individual
A2
kras status
normal
microscopic appearance
normal
organism part
colon
paris classification
normal PARIS classification
sample name
E-MTAB-6952:A2_normal
sampling site
normal tissue adjacent to pre-lesion
scientific_name
Homo sapiens
sex
male