|
| Status |
Public on Oct 27, 2016 |
| Title |
Matched Breast Primary Tumor |
| Sample type |
SRA |
| |
|
| Source name |
Invasive ductal carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Invasive ductal carcinoma
Sex: Female
developmental stage: Adult
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the fibroblast cell stock using phenol-chloroform extraction protocol, precipitated using ethanol precipitation protocol and resuspended in 1X TE buffer.
In brief, genomic DNA were fractionated by sonication, ligated to an adaptor and modified with bisulfite conversion protocol. It was then amplified with a PCR scheme designed to enrich AluYa5 and AluYb8, and finally size-fractionated using the E-gel Precast Agarose Electrophoresis System (Life Technologies). The prepared libraries were sequenced on the Ion-Torrent PGM platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
Trimming raw sequence reads smaller than 100-bp long out of a fastq file with a custome-made Python script
Mapping raw sequence reads to a custome-made database containing bisulfite-converted AluY sequences using Bowtie2
Grouping a number of sequence reads to each AluY5/Yb8 locus using a custome-made Perl script
Trimming out raw sequence reads for a given Alu locus that do not have a sufficient sequence coverage for DNA methylation analyses
Running a batch analysis of BiQanalyzerHT for DNA methylation levels of AluYa5/Yb8 with a custom-made Perl script
Genome_build: hg19
Supplementary_files_format_and_content: BED files showing methylation level of each sequenced locus
|
| |
|
| Submission date |
Oct 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Joomyeong Kim |
| E-mail(s) |
jkim@lsu.edu
|
| Organization name |
Louisiana State University
|
| Department |
Biological Sciences
|
| Street address |
202 Life Sciences Bldg
|
| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70803 |
| Country |
USA |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE74420 |
DNA methylation variation of human-specific Alu repeats |
|
| Relations |
| BioSample |
SAMN04219558 |
| SRA |
SRX1391722 |
