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Status |
Public on Aug 21, 2017 |
Title |
Gene expression of human bone marrow granulocytic differentiation stages |
Organism |
Homo sapiens |
Experiment type |
Non-coding RNA profiling by high throughput sequencing
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Summary |
Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis. This series only contains the RNAseq data obtained from successive stages of human granulocytic differentiation (myeloblasts, promyelocytes, metamyelocytes and neutrophils) which was obtained to validate the differentiation-dependent expression of LINC00173 in human granulopoiesis. To access the microarray data see GSE98633 and GSE98791.
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Overall design |
Myeloblasts/promyelocytes (n=4), metamyelocytes (n=3) and neutrophils (n=2) from healthy donor bone marrow were FACS-purified, prepped (Illumina TruSeq stranded) and sequenced on an Illumina HiSeq.
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Contributor(s) |
Klusmann J, Schwarzer A, Grasedieck S, Jongen-Lavrencic M, Kuchenbauer F |
Citation(s) |
28794406, 33054061 |
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Submission date |
May 16, 2017 |
Last update date |
Mar 01, 2021 |
Contact name |
Jan-Henning Klusmann |
E-mail(s) |
jan-henning.klusmann@kgu.de
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Organization name |
Goehte University Frankfurt
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Department |
Pediatric Hematology and Oncology
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Street address |
Theodor-Stern-Kai 7
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City |
Frankfurt |
ZIP/Postal code |
60590 |
Country |
Germany |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (9)
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Relations |
BioProject |
PRJNA386905 |
SRA |
SRP107179 |
Supplementary file |
Size |
Download |
File type/resource |
GSE98946_BM_raw_countmatrix_HTSeq.csv.gz |
715.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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