|
| Status |
Public on Jun 10, 2018 |
| Title |
Platelet Transcriptome Profiling in HIV and ABCC4 as a Biomarker of Platelet Activity |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The purpose of this study was to perform an unbiased RNA expression profile in platelets from HIV subjects under ART and healthy controls to identify a gene signature for the HIV hyperactive phenotype.
Methods: Rna-Sequencing was performed in leukocyte-depleted platelet RNA from 6 HIV subjects and 3 healthy controls. qRT–PCR validation was performed to validate our candidate transcripts.
Results: Across the 9 platelet samples, there was an average of 28.3 million mapped reads per sample with an average unique mapping rate of 91.6 %. Using a cut-off of normalized counts ≥1 across the 9 samples, we found 11988 expressed transcripts.
Conclusions: Our study represents a detailed analysis of platelet transcriptome generated by RNA-seq technology in HIV patients under ART. Further experiments identified the mechanism of our transcript target in mediating platelet activity and platelet cell effector function.
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| Overall design |
Platelet mRNA profiling in HIV subjects under ART vs helthy controls to identify candidate transcripts with differential expression.
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| Contributor(s) |
Marcantoni E, Allen N, Cambria MR, Dann R, Cammer M, Lhakhang T, O’Brien M, Kim B, Worgall T, Heguy A, Tsirigos A, Berger JS |
| Citation(s) |
30062189 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HL114978 |
Platelet Activity & Cardiovascular Events following Vascular Surgery |
NEW YORK UNIVERSITY SCHOOL OF MEDICINE |
Jeffrey S Berger |
| R24 OD018340 |
Restoring Biospecimen Research Resources Lost Due to Super Storm Sandy |
NEW YORK UNIVERSITY SCHOOL OF MEDICINE |
David E Levy |
|
| |
| Submission date |
Jun 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Stuart Berger |
| E-mail(s) |
jeffrey.berger@nyumc.org
|
| Organization name |
NYU Langone Medical Center
|
| Department |
Cardiology
|
| Lab |
707
|
| Street address |
522 First Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (9)
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| Relations |
| BioProject |
PRJNA389458 |
| SRA |
SRP108739 |
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