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Series GSE58999 Query DataSets for GSE58999
Status Public on Dec 01, 2014
Title Methylome remodeling in regional breast cancer metastasis [DNA methylation]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Genome-wide DNA methylation profiling of of 44 matched primary breast tumors and metastases.
We sought to characterize methylome remodeling during regional metastasis. We profiled the DNA methylome (n=44) and transcriptome (n=36) of matched primary breast tumors and regional metastases.
Overall design All paired samples (n = 88) were obtained following surgical resection at the MSKCC as part of routine clinical care. Tumors were obtained in accordance with Institutional Review Board policies at the MSKCC. Each sample was examined histologically by a breast pathologist and microdissected to achieve >70% tumor cell content. Genomic DNA was extracted using the DNeasy kit (Qiagen) as per the manufacturer’s instructions. Bisulphite converted DNA from the 44 primary breast tumors and matching metastases were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.
Contributor(s) Reyngold M, Chan TA
Citation(s) 25083786
Submission date Jul 01, 2014
Last update date Jun 14, 2020
Contact name Marsha Reyngold
Organization name Memorial Sloan-Kettering Cancer Center
Department Radiation Oncology
Lab Timothy Chan
Street address 1275 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (88)
GSM1423637 1_DNA_methylation
GSM1423638 2_DNA_methylation
GSM1423639 3_DNA_methylation
This SubSeries is part of SuperSeries:
GSE59000 Methylome remodeling in regional breast cancer metastasis
BioProject PRJNA254074

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58999_RAW.tar 183.1 Mb (http)(custom) TAR
GSE58999_unmethylated_and_methylated_signals.txt.gz 211.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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