|
| Status |
Public on Jun 08, 2021 |
| Title |
RET44 |
| Sample type |
genomic |
| |
|
| Source name |
rectal adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
response: pCR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from pre-treatment biopsies of rectal tissue using a phenol-chloroform-isoamyl alcohol (25:24:1) solution-based protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using the Illumina HiScan system with the standard recommended Illumina scanner setting
|
| Description |
naive biopsies
|
| Data processing |
data were processed using R language. Briefly, β values were normalized and batch effects were removed. Probes with low quality (detection p-value >0.05), mapped in X/Y chromosomes and cross-reactive were filtered out, as previously described by Pidsley R et al. (2016 - DOI: 10.1186/s13059-016-1066-1)
|
| |
|
| Submission date |
Jun 13, 2019 |
| Last update date |
Jun 08, 2021 |
| Contact name |
Luisa Matos do Canto |
| Organization name |
Vejle Hospital
|
| Department |
Biochemistry and Immunology
|
| Street address |
Beriderbakken 4
|
| City |
Vejle |
| ZIP/Postal code |
7100 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23976 |
| Series (1) |
| GSE132668 |
DNA methylation-based classifier to predict pathological complete response to neoadjuvant chemoradiotherapy in locally advanced rectal carcinomas. |
|
