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Sample GSM1715443 Query DataSets for GSM1715443
Status Public on Jul 25, 2015
Title N1 [RRBS-seq]
Sample type SRA
 
Source name normal breast epithelium
Organism Homo sapiens
Characteristics age (yrs): 44
race: White
tissue: normal breast epithelial organoid
Extracted molecule genomic DNA
Extraction protocol DNA was purified using the DNeasy Blood and Tissue Kit (Qiagen). Only DNA samples with 260/280 ratios greater than 2.0 were processed for library construction.
1ug of genomic DNA was digest with MspI, end-repaired, 3-prime adenylated, and methylated adapters were ligated to the fragments. Adapter-ligated fragments corresponding to an insert size of 40bp to 220bp were excised and eluted from agarose gels, bisulfite treated and amplified by PCR.
Reduced Representation Bisulfite Sequencing analysis (RRBS; Meissner et al., Nature 2008).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2000
 
Description processed data column: A1.2
Data processing We performed 36 nt single end read Illumina HiSeq2000 platform.
Illumina Casava1.7 software used for basecalling.
The bisulfite treated sequencing reads were mapped to the human reference genome (hg19) by Bismark software.
Promoter regions were calculated based on RefSeq gene annotations, such that the region starts 2 kb upstream of the annotated transcription start site and extends to 500 downstream of the TSS. CpG islands were downloaded from UCSC genome annotation database assembled by NCBI (hg19).
To identify differentially methylated sites first we filtered samples based on read coverage ≥ 20. And the significant differentially methylated CpGi sites (DMC) were identified when the difference of methylation percentages between normal breast epithelia and DCIS were greater than 0.25 and q-value <0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include methylated reads number for each Sample
 
Submission date Jun 18, 2015
Last update date May 15, 2019
Contact name C. Marcelo Aldaz
E-mail(s) maaldaz@mdanderson.org
Phone 512-237-9530
Organization name The University of TX M.D. Anderson Cancer Center
Department Molecular Carcinogenesis
Lab Aldaz Lab
Street address POB 389
City Smithville
ZIP/Postal code 78957
Country USA
 
Platform ID GPL11154
Series (2)
GSE69993 A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS) [RRBS-seq]
GSE69994 A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS)
Relations
BioSample SAMN03782075
SRA SRX1065192

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

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