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Series GSE98946 Query DataSets for GSE98946
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
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.
 
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.
 
Contributor(s) Klusmann J, Schwarzer A, Grasedieck S, Jongen-Lavrencic M, Kuchenbauer F
Citation(s) 28794406, 33054061
Submission date May 16, 2017
Last update date Mar 01, 2021
Contact name Jan-Henning Klusmann
E-mail(s) jan-henning.klusmann@kgu.de
Organization name Goehte University Frankfurt
Department Pediatric Hematology and Oncology
Street address Theodor-Stern-Kai 7
City Frankfurt
ZIP/Postal code 60590
Country Germany
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (9)
GSM2628191 BM1_Blasts
GSM2628192 BM1_Metamyelocytes
GSM2628193 BM1_Neutrophiles
Relations
BioProject PRJNA386905
SRA SRP107179

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE98946_BM_raw_countmatrix_HTSeq.csv.gz 715.1 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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