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| Status |
Public on May 06, 2020 |
| Title |
ASEP: gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Allele-specific expression (ASE) quantifies the relative expression of two alleles in a diploid individual, and such expression imbalance potentially contributes to phenotypic variation and disease pathophysiology among individuals. We developed ASEP, a method that is able to detect gene-level ASE under one condition, as well as, ASE difference between two conditions (e.g., pre- vs post-treatment) across individuals. Application of ASEP to human macrophage RNA-seq dataset has illustrated its ability to uncover ASE / differential ASE genes related to cardiometabolic traits.
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| Overall design |
Human peripheral blood mononuclear cell (PBMC)-derived macrophages (HMDM) and M1-polarized HMDM were sequenced by Illumina HiSeq 2500 with poly-A selection
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| Contributor(s) |
Zhang H, Xue C |
| Citation(s) |
32392242 |
| |
| Submission date |
Apr 30, 2020 |
| Last update date |
Aug 05, 2020 |
| Contact name |
Chenyi Xue |
| Organization name |
Columbia University
|
| Street address |
630 W 168th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (96)
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| Relations |
| BioProject |
PRJNA629498 |
| SRA |
SRP259314 |
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