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Sample GSM3263225 Query DataSets for GSM3263225
Status Public on Jun 30, 2023
Title d9984c
Sample type SRA
 
Source name human breast cancer tissue
Organism Homo sapiens
Characteristics gender: female
methylated fraction: TNBC
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from normal breast and breast cancer samples with a Qiagen Puregene kit following the manufacturer's protocol. Approximately 1 µg genomic DNA was sheared to 200- to 400-bp fragments using a Covaris LE220 sonicator. The sonicated genomic DNA was immunoprecipitated with human MBD2 protein coupled with paramagnetic Dynabeads M-280 Streptavidin via a biotin linker using a MethylMiner Methylated DNA Enrichment Kit.
Libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina HiSeq 2000
 
Description The methylated fraction from TNBC
Data processing Paired-end 100bp sequence reads were aligned to the hg19 genome reference using bowtie.
The methylation abundance within region of interest (ROI) was estimated by MEDIPS R package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_Merged_Samples_averaged_read_counts_ROI_CDS.txt is a tab-delimited text file that contains the read counts of gene symbols located in CDS regions and processed_Merged_Samples_averaged_read_counts_ROI_PROMOTER.txt is a tab-delimited text file that contains the read counts of gene symbols located in promoter regions.
 
Submission date Jul 10, 2018
Last update date Jun 30, 2023
Contact name Jong Hoon Park
E-mail(s) parkjh@sm.ac.kr
Phone 822-710-9414
Organization name Sookmyung Women's university
Lab Molecular Medicine Lab
Street address Cheongpa-ro 47-gil 100, Yongsan-gu,
City Seoul
ZIP/Postal code 04310
Country South Korea
 
Platform ID GPL11154
Series (1)
GSE116877 Genome-wide methylation analysis of human breast cancer subtype group (Luminal A, Luminal B, HER2+ and TNBC)
Relations
BioSample SAMN09642285
SRA SRX4379385

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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