|
| 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 |
