title: S17
organism: Homo sapiens
description: 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).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2018-11-23T17:04:22Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-06-27T15:33:30Z
attributes.tag: External Id
attributes.value: SAMEA4766566
attributes.tag: INSDC center name
attributes.value: UZH
attributes.tag: INSDC first public
attributes.value: 2018-11-23T17:04:22Z
attributes.tag: INSDC last update
attributes.value: 2018-06-27T15:33:30Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-6952:S17
attributes.tag: age
attributes.value: 53
attributes.tag: braf status
attributes.value: BRAF mutation c.1799T>A (V600E)
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: clinical information
attributes.value: no dysplasia
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: Colon Sessile Serrated Adenoma/Polyp
attributes.tag: individual
attributes.value: S17
attributes.tag: kras status
attributes.value: wild type KRAS
attributes.tag: microscopic appearance
attributes.value: SSA/P
attributes.tag: number of lesions at study colonoscopy
attributes.value: 1 lesions at study colonoscopy
attributes.tag: organism part
attributes.value: colon
attributes.tag: paris classification
attributes.value: PARIS classification 0-IIa
attributes.tag: sample name
attributes.value: E-MTAB-6952:S17
attributes.tag: sampling site
attributes.value: pre-lesion
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: sex
attributes.value: female