|
| Status |
Public on Oct 22, 2014 |
| Title |
Human Female low BMD_methylation_3 |
| Sample type |
SRA |
| |
|
| Source name |
Healthy female_low_BMD
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood monocytes
tissue: blood
Sex: female
|
| Treatment protocol |
Monocyte isolation,A monocyte negative isolation kit (Order No. 130-091-153, Miltenyi Biotec Inc., Auburn, CA, USA) was used to isolate circulating monocytes from 150mL whole blood following the procedures
|
| Growth protocol |
One hundred and fifty milliliters of peripheral blood were drawn for each selected subject.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the freshly isolated PBMs. The concentration of DNA was assessed by using Qubit 2.0 Fluorometer (Invitrogen,).
1.5μg of sonicated DNA was end-repaired, 3’A added, and ligated to single-end adapters following the standard Illumina genomic DNA protocol.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ams_D6
|
| Data processing |
The completed libraries were quantified and checked for quantity with Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System.
Subsequently sequenced on Illumina HiSeq 2000 (with single-end, 49bp reads)
Sequencing reads that passed through the HiSeq 2000 quality filter were aligned to the human genome reference sequence (GRCh37/hg19) using SOAP (Version 2.20).
DNA methylation profiles were inferred from the uniquely aligned reads by using the MEDIPS analysis package
the corresponding genomic locations were obtained from the UCSC Genome Brower.
Genome_build: hg19
Supplementary_files_format_and_content: pvalues for methylation status
|
| |
|
| Submission date |
Oct 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
shishi min |
| E-mail(s) |
[email protected]
|
| Phone |
15580884581
|
| Organization name |
Hunan Normal University
|
| Department |
College of life sciences
|
| Lab |
Laboratory of Molecular and Statistical Genetics
|
| Street address |
Lu shan road
|
| City |
Chang sha |
| State/province |
Hunan |
| ZIP/Postal code |
410000 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE62588 |
Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk [methylome] |
| GSE62589 |
Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk |
|
| Relations |
| BioSample |
SAMN03135162 |
| SRA |
SRX738244 |
