|
| Status |
Public on Feb 14, 2019 |
| Title |
Blood_NAFLD_01 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
circumstances: blood draw
diagnosis: Non-alcoholic fatty liver disease
Sex: Female
age: 52
bmi: 47.3
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
Diluted DNA was bisulfite converted using the EZ DNA Methylation Lightning kit (Zymo) according to the manufacturer’s instructions. WGBS libraries were prepared using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
VMNS012A
|
| Data processing |
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to hg38 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Genome_build: hg38
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding
|
| |
|
| Submission date |
Jul 24, 2018 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Charles E Mordaunt |
| E-mail(s) |
mordauntcharles@gmail.com
|
| Organization name |
University of California, Davis
|
| Department |
Medical Microbiology and Immunology
|
| Lab |
LaSalle Lab
|
| Street address |
3318 Tupper Hall, One Shields Ave
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE117593 |
Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers |
|
| Relations |
| BioSample |
SAMN09709890 |
| SRA |
SRX4452770 |
