|
| Status |
Public on Sep 21, 2018 |
| Title |
Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [scRNA] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
New techniques for single-cell analysis have led to insights into hematopoiesis and the immune system, but the ability of these techniques to cross-validate and reproducibly identify the biological variation in diverse human samples is currently unproven. We therefore performed a comprehensive assessment of human bone marrow cells using both single-cell RNA sequencing and multiparameter flow cytometry from twenty healthy adult human donors across a broad age range. These data characterize variation between healthy donors as well as age-associated changes in cell population frequencies. Direct comparison of techniques revealed discrepancy in the quantification of T lymphocyte and natural killer cell populations. Orthogonal validation of immunophenotyping using mass cytometry demonstrated good correlation with flow cytometry. Technical replicates using single-cell RNA sequencing matched robustly, while biological replicates showed variation. Given the increasing use of single-cell technologies in translational research, this resource serves as an important reference dataset and highlights opportunities for further refinement.
[Funding source]
Project Number: 1ZIAHL006163-05
Contact PI / Project Leader: HOURIGAN, CHRISTOPHER
Title: DETECTION, PREVENTION AND TREATMENT OF ACUTE MYELOID LEUKEMIA (AML) RELAPSE.
Awardee Organization: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
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| Overall design |
Using standard operating procedures, mononuclear cells from 20 healthy donors' bone marrow aspirates were isolated using Ficoll density gradient separation and cryopreserved in 90% FBS/ 10% DMSO for storage in 72 liquid nitrogen. scRNAseq was performed using 10X Genomics Single Cell 3’ Solution, version 2 according to manufacturer’s instructions (protocol rev A). Libraries were sequenced on HiSeq3000. Droplet-based scRNAseq of bone marrow mononuclear cells for all donor samples was performed with goal minimum sequencing depth of 50,000 reads/cell and detected a mean of 880 genes/cells (range 575-1,390 gene/cell).
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| Web link |
https://doi.org/10.1101/416750
|
| |
|
| Contributor(s) |
Oetjen KA, Gui G, Hourigan CS |
| Citation(s) |
30518681 |
| Submission date |
Sep 19, 2018 |
| Last update date |
Dec 23, 2018 |
| Contact name |
Christopher Hourigan |
| E-mail(s) |
christopher.hourigan@nih.gov
|
| Phone |
3014510257
|
| Organization name |
National Heart Lung and Blood Institute, NIH
|
| Department |
Hematology Branch
|
| Lab |
Myeloid Malignancies
|
| Street address |
Room 10CRC 5-5130, 10 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
|
| Samples (25)
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| This SubSeries is part of SuperSeries: |
| GSE120446 |
Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry |
|
| Relations |
| BioProject |
PRJNA492227 |
| SRA |
SRP162214 |
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