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Status |
Public on Jun 16, 2021 |
Title |
HER2 -positive breast cancer (microdissected, cancer cell) 01 |
Sample type |
genomic |
|
|
Source name |
3-2C
|
Organism |
Homo sapiens |
Characteristics |
gender: Female age: 54 clinical tumor stage: T3 clinical nodal stage: N1 clinical stage: IIIA histology: Invasive ductal carsinoma er: Negative pgr: Negative chemotherapy effect: Grade3
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Specimen was obtained from each patient by core needle biopsy of a primary tumor before starting neoadjuvant therapy, and fixed using the PAXgene Tissue System (Qiagen, Hilden, Germany) and embedded in low-melting paraffin. Cancer cells or stroma cells were purified by the Leica LMD7000 system (Leica, Wetzlar, Germany) using 10 slices of 10-μm sections of block. This was conducted by an experienced pathologist (S. F.). Genomic DNA was extracted by a PAXgene DNA kit (Qiagen).
|
Label |
Cy5 and Cy3
|
Label protocol |
Standard Illumina Protocol
|
|
|
Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.
|
Scan protocol |
Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).
|
Description |
clinical specimen, breast tissues
|
Data processing |
Genome Studio software (V2011.1 Methylation module 1.9.0) was used. Beta values were obtained after background correction and normalization to internal controls.
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|
|
Submission date |
Jun 15, 2021 |
Last update date |
Jun 16, 2021 |
Contact name |
Satoshi Yamashita |
E-mail(s) |
syamashi@maebashi-it.ac.jp
|
Organization name |
National Cancer Center Research Institute
|
Street address |
Tsukiji 5-1-1
|
City |
Chuo-ku |
State/province |
Tokyo |
ZIP/Postal code |
104-0045 |
Country |
Japan |
|
|
Platform ID |
GPL13534 |
Series (1) |
GSE178235 |
Genome-wide DNA methylation analysis of HER2-positive breast cancer and stroma |
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