|
| Status |
Public on Oct 12, 2016 |
| Title |
Control_1_IP_Male |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: blood cells
group: non-exposed
Sex: Male
|
| Treatment protocol |
Two different population
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood using DNeasy Blood & Tissue kit (Qiagen, Valencia, CA)
MIRA-seq libraries were firstly constructed using Illumina’s TruSeq DNA Sample Preparation Kit-Set A/B (P/N FC-121-1001/1002). Briefly, ends of MIRA enriched methylated DNA (~40-100ng) were repaired and an ‘A’ base added to the 3’ for ligating DNAs to the adapters. Following ligation, the DNA resolved in 2% agarose gel was size-selected, with200±25bp fragments for library amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Library strategy: MIRA-seq
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using bwa
bed files were generated from bam files using the bedtools package
Further analysis based on bed files were done using the MEDIPS R package
Genome_build: hg19
Supplementary_files_format_and_content: Bed and wig with normalized reliative methylation score (rms) files for MIRA-Seq data.
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE73931 |
Aberrant blood DNA methylation reveals reproductive hormone imbalances in firefighters |
|
| Relations |
| BioSample |
SAMN04160428 |
| SRA |
SRX1331076 |
