|
| Status |
Public on May 10, 2020 |
| Title |
Paired Adjacent Normal sample from P2032_N patient |
| Sample type |
genomic |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Normal
Stage: IIA
gender: Female
age: 67
location: Left
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from colon tissue by the phenol-chloroform procedure, quantified using a Nano Drop ND 2000c spectrophotometer (NanoDrop Thermo scientific, Wilmington, DE) and stored at 4ºC.
|
| Label |
Cy3, Cy5
|
| Label protocol |
Cy3 and Cy5; Standard Illumina labelling protocol
|
| |
|
| Hybridization protocol |
Bisulfite conversion of DNA (200-500 ng) was performed according to the manufacturer’s recommendations for the Illumina Infinium Assay (EZ DNA methylation kit. Zymo Research. Cat. No. D5004).
|
| Scan protocol |
Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting
|
| Description |
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2032_N
|
| Data processing |
Methylation level at each locus was measured using β values calculated based on Illumina’s standard, using the average probe intensity for the methylated and unmethylated alleles
matrix processed value definition: Average Beta
|
| |
|
| Submission date |
May 10, 2019 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Victor Moreno |
| E-mail(s) |
v.moreno@iconcologia.net
|
| Organization name |
Catalan Institute of Oncology
|
| Department |
Oncology Data Analytics Program
|
| Street address |
Granvia 199
|
| City |
L'Hospitalet de Llobregat |
| State/province |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE131013 |
Methylation data from healthy, adjacent normal and tumor colon cells |
| GSE166427 |
Healthy, adjacent normal and tumor colon cells |
|
