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Genome-wide analysis of miRNA-mRNA interactions in the marrow microenvironment (HTS)

ABSTRACT: We report genome-wide analysis of miRNA-mRNA interactions in the hematopoietic marrow microenvironment (ME) by employing the biochemical technique. High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation or HITS-CLIP. Specifically, we analyzed 3 kinds of stromal cells (two human stromal cell lines named HS5 and HS27a and primary mesenchymal stromal cells (MSC) from normal donors) and two types of endothelial cells (TrBMEC, a human bone marrow endothelial cell line) and HUVEC (Human Umbilical Vein Endothelial Cells).

ORGANISM(S): Homo sapiens

PROVIDER: GSE41272 | GEO | 2013/09/01

SECONDARY ACCESSION(S): PRJNA176418

REPOSITORIES: GEO

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Genome-wide analysis of miRNA-mRNA interactions in the marrow microenvironment (HTS)

Project description:We report genome-wide analysis of miRNA-mRNA interactions in the hematopoietic marrow microenvironment (ME) by employing the biochemical technique. High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation or HITS-CLIP. Specifically, we analyzed 3 kinds of stromal cells (two human stromal cell lines named HS5 and HS27a and primary mesenchymal stromal cells (MSC) from normal donors) and two types of endothelial cells (TrBMEC, a human bone marrow endothelial cell line) and HUVEC (Human Umbilical Vein Endothelial Cells). Immune precipitation (IP) of Argonaut proteins (AGO1-4) was performed by anti-AGO monoclonal antibody 2A8. IP was performed on cells cross-linked by short-wave ultraviolet radiation (UV) 365 nM. Protocol was modified from as originally published by Chi et al Nature. 2009 Jul 23;460(7254):479-86.

2013-09-01 | E-GEOD-41272 | biostudies-arrayexpress

Global gene expression analysis of CDCP1, KDM3B, and SDC1 knockdown in human marrow stromal cells

Project description:To elucidate functions of CDCP1, KDM3B and SDC1 molecules in HS5 human marrow stromal cells, global gene expression profiles were obtained and analyzed after knocking down the gene transcripts by using siRNA technology. Global gene expression profiles were obtained from HS5 marrow stromal cells after knocking down mRNA of CDCP1, KDM3B or SDC1 by using siRNA technology.

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Transcription profiling by array of human bone marrow stromal cells lines cultured with monocytes to investigate interactions in the hematopoietic microenvironment

Project description:The hematopoietic microenvironment consists of non-hematopoietic derived stromal elements and hematopoietic derived monocytes and macrophages which interact and function together to control the proliferation and differentiation of early blood-forming cells. Two human stromal cell lines (HS-5 and HS-27a) representing distinct functional components of this microenvironment have been extensively characterized and shown to influence monocyte gene expression. This series of gene expression profiles is intended to extend the previous studies and identify which gene expression changes may require cell-cell contact or occur in the stromal cells as a result of monocyte influence;or in the monocytes as a result of stormal influences. Experiment Overall Design: Two human bone marrow stromal cell lines (HS5 and HS27a) were cultured with and without monocytes (CD14+ cells) from 2 different donors. Experiment Overall Design: culture condition: stroma no monocytes: HS5-1, HS5-2, HS27a-1, HS27a-2 Experiment Overall Design: culture condition: stroma with monocytes: HS5-MO-1, HS5-MO-2, HS27a-MO-1, HS27a-MO-2 Experiment Overall Design: donor: donor 3: HS5-MO-1, HS27a-MO-1 Experiment Overall Design: donor: donor 4: HS5-MO-2, HS27a-MO-2 Experiment Overall Design: cell line: HS5: HS5-1, HS5-2, HS5-MO-1, HS5-MO-2 Experiment Overall Design: cell line: HS27a: HS27a-1, HS27a-2, HS27a-MO-1, HS27a-MO-2

2008-04-07 | E-GEOD-10595 | biostudies-arrayexpress

Global gene expression analysis of CDCP1, KDM3B, and SDC1 knockdown in human marrow stromal cells

2013-12-10 | GSE53199 | GEO

Human Ago2-HITS-CLIP

Project description:mRNA and microRNA profile of Endothelial cells (HUVEC and HUAEC) were generated by HITS-CLIP assay, in triplicate

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Transcription profiling of human monocytes grown in CM from functionallu distinct cell lines HS5 and HS27a

Project description:The bone marrow microenvironment is a complex mixture of cells that function in concert to regulate hematopoiesis. Cellular components include fixed nonhematopoietic stromal elements as well as monocytes and resident macrophages, which are derived from the hematopoietic stem cells. Although these monocyte-lineage cells are reported to modify stromal cell function, the reverse also occurs. Given the secretory capability of the monocyte/macrophage and their various potential functions, it is not surprising that stromal cells contained within a particular niche can modify monocyte gene expression and functional maturation. Experiment Overall Design: Monocytes were isolated from peripheral blood mononuclear cells from 2 different normal donors and cultured for 48h in conditioned medium (CM). The CM was collected from each of two functionally distinct human bone marrow stromal cell lines (HS5 and HS27a) representing different compartments of the bone marrow microenvironment (Roecklein BA, Torok-Storb B. Blood. 1995;85:997-1005). Four samples were analyzed, with two biological replicates for each CM.

2008-04-06 | E-GEOD-9390 | biostudies-arrayexpress

Comparison of Trabecular Meshwork-Derived Cells (TMDCs) with other somatic Cell Types

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2012-05-01 | GSE28679 | GEO

Global gene expression profile of human peripheral blood-derived endothelial colony-forming cells is similar to coronary artery and umbilical vein endothelial cells

Project description:We performed a transcriptome-wide study to compare gene expression profiles of ECFC, human coronary artery endothelial cells (HCAEC) and human umbilical vein endothelial cells (HUVEC) utilising subcutaneous adipose tissue-derived stromal vascular fraction (SAT-SVF) as a negative control population. Baseline gene expression in ECFC fully corresponds to their endothelial specification and may contribute to the basement membrane organisation, fulfilling the requirements for the suitable cell population for in vitro pre-endothelialisation of tubular scaffolds.

2019-05-31 | GSE131995 | GEO

Endothelium-derived stromal cells contribute to bone marrow niche formation

Project description:Comprehensive transcriptional characterization of bone marrow stromal cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during niche formation.Here, we identify a rare subset of cells in the human fetal BM that co-express endothelial and stromal markers, including low-affinity nerve growth factor receptor (LNGFR/CD271). They display transcriptional reprogramming consistent with endothelial-to-mesenchymal transition (EndoMT), reflected in their potential to generate stromal cells with in vivo BM niche forming capacity.

| EGAS00001004946 | EGA

Comparison of Trabecular Meshwork-Derived Cells (TMDCs) with other somatic Cell Types

2012-04-30 | E-GEOD-28679 | biostudies-arrayexpress

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