GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE120221 Query DataSets for GSE120221
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
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).
Web link
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
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
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (25)
GSM3396161 Bone marrow A
GSM3396162 Bone marrow B
GSM3396163 Bone marrow C1
This SubSeries is part of SuperSeries:
GSE120446 Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry
BioProject PRJNA492227
SRA SRP162214

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120221_RAW.tar 300.0 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap