NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5384983 Query DataSets for GSM5384983
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.
 
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

Data table header descriptions
ID_REF
VALUE Average Beta
2C.Signal_A
2C.Signal_B
2C.Detection Pval

Data table
ID_REF VALUE 2C.Signal_A 2C.Signal_B 2C.Detection Pval
cg00000029 0.1666207 1883.768 396.6224 0
cg00000108 0.9570082 137.2092 5280.334 0
cg00000109 0.8962738 57.1705 1358.073 0
cg00000165 0.8656067 162.9359 1693.53 0
cg00000236 0.8647981 102.9069 1297.863 0
cg00000289 0.4750174 600.2902 633.6401 0
cg00000292 0.534061 4719.425 5524.042 0
cg00000321 0.1040637 4573.64 542.847 0
cg00000363 0.4955746 4173.446 4198.463 0
cg00000622 0.01458972 13800.96 205.8138 0
cg00000658 0.8241265 1426.404 7152.583 0
cg00000714 0.08427481 19080.65 1765.209 0
cg00000721 0.9300563 154.3604 3382.281 0
cg00000734 0.05103533 9407.405 511.3084 0
cg00000769 0.02484274 10216.61 262.8221 0
cg00000807 0.673905 5456.924 11483.89 0
cg00000884 0.8285819 320.1548 2030.898 0
cg00000905 0.07510166 1100.532 97.48309 0
cg00000924 0.5303636 4282.07 4948.701 0
cg00000948 0.8294291 1892.344 9688.1 0

Total number of rows: 485577

Table truncated, full table size 19378 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.