|
| Status |
Public on Aug 27, 2024 |
| Title |
tumor tissue [CIM014] |
| Sample type |
genomic |
| |
|
| Source name |
inflammatory breast cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: CIM014
tissue: inflammatory breast cancer tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 24 fresh frozen macrodissected IBC tissue biopsies and six surrounding normal breast frozen tissues using the QIAsymphony kit (Qiagen, Valencia, CA, USA).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Cy5 and Cy3
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was hybridised to Infinium Human Methylation EPIC BeadChip according to the manufacturer’s recommendations.
|
| Scan protocol |
The Illumina HiScan system was used to scan the beadchip platform.
|
| Description |
CIM014
|
| Data processing |
Data processing was performed with R software. Briefly, probes with low quality (detection p-value > 0.05), mapped in X/Y chromosomes or to SNPs, and cross-reactive were filtered out using the minfi package. Differences in Type-I and Type-II probes and normalization of the β values were adjusted using the Beta MIxture Quantile dilation (BMIQ) method. Batch effect was corrected with ComBat function from sva package (v.3.44.0).
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Fabio Albuquerque Marchi |
| E-mail(s) |
fabio.marchi@fm.usp.br
|
| Organization name |
ICESP
|
| Department |
CTO
|
| Street address |
Av Dr Arnaldo
|
| City |
Sao Paulo |
| ZIP/Postal code |
01246-000 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE238092 |
Epigenome-wide DNA methylation analysis in inflammatory breast cancer |
|
