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
2018-06-27T15:33:28Z
External Id
SAMEA4766540
INSDC center name
UZH
INSDC first public
2018-11-23T17:04:22Z
INSDC last update
2018-06-27T15:33:28Z
INSDC status
public
Submitter Id
E-MTAB-6952:S12_normal
age
49
braf status
normal
broker name
ArrayExpress
common name
human
disease
Colon Sessile Serrated Adenoma/Polyp
individual
S12
kras status
normal
microscopic appearance
normal
organism part
colon
paris classification
normal PARIS classification
sample name
E-MTAB-6952:S12_normal
sampling site
normal tissue adjacent to pre-lesion
scientific_name
Homo sapiens
sex
male