|
Status |
Public on Feb 03, 2015 |
Title |
CRC2_010_Adenoma1 |
Sample type |
genomic |
|
|
Source name |
Colon primary tissue
|
Organism |
Homo sapiens |
Characteristics |
Sex: female patient: 010 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_010AD1 Patient 010 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 |
|