|
Status |
Public on Jun 30, 2023 |
Title |
d2195n |
Sample type |
SRA |
|
|
Source name |
human breast cancer adjacent normal 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.
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|
|
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.
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|
|
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 |
SAMN09642284 |
SRA |
SRX4379386 |