|
| Status |
Public on Feb 07, 2024 |
| Title |
Control154 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
cell type: Blood
genotype: Healthy Control
chip antibody: 5-methylcytosine (5-mC) Antibody
|
| Treatment protocol |
whole blood
|
| Growth protocol |
whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from 0.5 ml of whole blood using Qiagen DNeasy Blood & Tissue Kits.
The total genomic DNA was ultrasonic fragmented to 150-300 bp using Covaris M220 machine, following by end-repair and A-tailing using Kapa HyperPrep Kit (Kapa Biosystems). The A-tailed DNA were then ligated with the NEBNext adaptor, purified with AMPure XP beads (Beckman Coulter) and then digested with USER enzyme (New England BioLabs) to release the dU loop structure of the adapter. The products were further purified using Qiagen MinElute PCR Purification Kit. Subsequently, MeDIP immunoprecipitation using MagMeDIP kit (Diagenode) was performed following previously described protocols. An average of 100ng of fragmented DNA were used for the MeDIP immunoprecipitation
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The sequencing quality of the fastq files of MeDIP-seq was assessed before mapping to the hg19 using BWA. PCR duplicates were removed if both ends were at the same positions. Total number of mapped reads, mapping quality and fragment size were evaluated. For samples passing quality cut-offs, we proceeded to identification of differential methylation using both QSEA package in the R BioConductor and MACS2 and obtained the union of the two results as tentative candidates for downstream analysis. For each identified candidate, methylation level was quantified using featureCounts and normalized to Reads Per Million mapped reads (RPM). These normalized RPM counts cross different samples were further employed to extract the DMRs between two groups, e.g. pre-AML/MDS cases and controls or pre-AML and pre-MDS.
Assembly: hg19
Supplementary files format and content: log2 normalized counts (10 bg)
|
| |
|
| Submission date |
Jan 12, 2024 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Qiaoyang Sun |
| E-mail(s) |
[email protected]
|
| Organization name |
National Neuroscience Institute
|
| Department |
Neurology
|
| Street address |
20 College Rd
|
| City |
Singapore |
| ZIP/Postal code |
169856 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE253126 |
A Pre-Leukemic DNA Methylation Signature in Healthy Individuals Associated with Risk of Myeloid Malignancy |
|
| Relations |
| BioSample |
SAMN39423973 |
| SRA |
SRX23204575 |
