|
| Status |
Public on Feb 03, 2015 |
| Title |
CRC2_009_Adenoma4 |
| Sample type |
genomic |
| |
|
| Source name |
Colon primary tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
patient: 009
tissue: adenoma tissue
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
according to Qiagen AllPrep kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Bisulfite conversion used the EZ-Gold kit (Zymo)
|
| |
|
| Hybridization protocol |
followed the Infinium-II-Assay guide
|
| Scan protocol |
Slides were scanned on an iScan
|
| Description |
Sample name: CRC2_009Ad4
Patient 009 adenoma tissue
|
| Data processing |
BeadStudio was used to obtain the raw Signal_A and Signal_B values which were then read into R and processed using a custom script. Subsequently, locus methylation was calculated as an M value (log ratio of the Methylated versus Unmethylated channels) and separate quartile normalisation was applied to the probes annotated in the green or red channel.
|
| |
|
| Submission date |
May 17, 2013 |
| Last update date |
Sep 14, 2015 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE47071 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [Methylation27 Array] |
| GSE47592 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer |
|
