|
| Status |
Public on May 31, 2024 |
| Title |
genomic DNA from JVE109 |
| Sample type |
genomic |
| |
|
| Source name |
CRC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CRC cell line
|
| Biomaterial provider |
LUMC
|
| Treatment protocol |
All cells were maintained in absence of drug
|
| Growth protocol |
All cells were maintained in the media recommanded by supplier
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted Maxwell RSC Blood DNA kit (Promega)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina labelling protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip microarray using standard Illumina Infinium HD methylation protocol
|
| Scan protocol |
Arrays were imaged using iScan with the standard recommended Illumina scanner setting
|
| Description |
Parental CRC cell line grown in vitro without any treatment
|
| Data processing |
EPIC raw data (IDAT files) were processed using the minfi R Bioconductor package and corresponding annotation packages. In each sample, probes with detection p-value > 0.05 were masked in the RGChannelSet. In addition, cross-reactivity probes and probes matching SNPs at the target CpG site were filtered using previously published lists. Then, methylation and unmethylation signals were obtained for each CpG site using the preprocessNoob function and beta-values were computed. Results obtained in all samples were subsequently merged in a single beta-matrix and CpG sites that are located on sex chromosomes or chrM were excluded.
|
| |
|
| Submission date |
Dec 06, 2022 |
| Last update date |
May 31, 2024 |
| Contact name |
Federica Di Nicolantonio |
| E-mail(s) |
federica.dinicolantonio@unito.it
|
| Organization name |
University of Torino
|
| Department |
Department of Oncology
|
| Lab |
Laboratory of Cancer Epigenetics
|
| Street address |
Candiolo Cancer Institute FPO-IRCCS, SP142, km 3.95
|
| City |
Candiolo |
| State/province |
Torino |
| ZIP/Postal code |
10060 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE220197 |
Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer |
|
