GEO DataSets

(Submitter supplied) Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

247 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL18573 GPL13497

259 Samples

Download data: TXT

(Submitter supplied) Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

6 Samples

Download data: TXT

(Submitter supplied) Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) Background: Bone marrow stromal cells (BMSCs) have classically been cultured in media supplemented with 20% fetal bovine serum (FBS). As an alternative to FBS, pooled solvent detergent apheresis platelets, HPGF-C18, was evaluated for BMSC culture. Methods: A comparison of passage 2 BMSC growth revealed that 10% HPGF-C18 produced similar cell numbers as 20% FBS. Marrow aspirates from 5 healthy subjects were cultured for 4 passages in 10% HPGF-C18 or 20% FBS and were analyzed for proliferation, colony formation efficiency (CFE), surface marker expression, suppression of mixed lymphocyte reactions (MLRs), global gene and microRNA expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16297

22 Samples

Download data: TXT

(Submitter supplied) Bone marrow stromal cells (BMSCs) can be expanded by serial passage, but expansion is limited by cell senescence.  The nature of changes associated with BMSC serial passages was assessed. Transcriptome analysis of 10 early and 15 late passage samples from 5 subjects revealed 2193 differentially expressed genes; those highly expressed in early passage cells were overrepresented in skeletal system development, embryonic morphogenesis, tube morphogenesis, etc, while those highly expressed in the late passage BMSCs were overrepresented in nucleosome assembly; chromatin assembly, DNA packaging, etc. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

57 Samples

Download data: TXT

(Submitter supplied) Human bone marrow derived mesenchymal stromal cells (BMSCs) represent a putative cell source candidate for tissue engineering based strategies to repair cartilage and bone. However, traditional isolation of BMSCs by their preference to adhere to plastic leads to very heterogeneous cell populations and may account for high inter-donor variability and unpredictability of chondrogenic differentiation out-come. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

34 Samples

Download data: CSV

(Submitter supplied) Ex vivo expansion of Bone Marrow Stromal Cells (BMSC) is required to obtain clinical dose for cellular therapy, and different labs use different confluence in their practice, however, the impacts of 100% confluence on the biological properties of BMSC remain controversial. In this study, we detected the changes occurred to BMSCs when they reached 100% confluence, including viability, population doubling time (PDT), apoptosis, colony formation, immunosuppression, proteins in the culture supernatant, and surface markers; we also performed gene expression profiling and microRNA profiling on 50%, 80% and 100% confluent BMSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

15 Samples

Download data: TXT

(Submitter supplied) Ex vivo expansion of Bone Marrow Stromal Cells (BMSC) is required to obtain clinical dose for cellular therapy, and different labs use different confluence in their practice, however, the impacts of 100% confluence on the biological properties of BMSC remain controversial. In this study, we detected the changes occurred to BMSCs when they reached 100% confluence, including viability, population doubling time (PDT), apoptosis, colony formation, immunosuppression, proteins in the culture supernatant, and surface markers; we also performed gene expression profiling and microRNA profiling on 50%, 80% and 100% confluent BMSCs. more...

Organism:

human gammaherpesvirus 4; Betapolyomavirus macacae; Rattus norvegicus; Mus musculus; Human gammaherpesvirus 8; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19084

15 Samples

Download data: GPR

(Submitter supplied) We performed small RNA sequencing on telomerized human bone marrow skeletal (stromal or mesenchymal) stem cells (hMSC-TERT) at various timepoints during differentiated into osteoblasts

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

24 Samples

Download data: TXT

(Submitter supplied) The Wharton’s jelly of the human umbilical cord contains a population of mesenchymal stem cells that are unique and possess significant clinical utility. Known as human Wharton’s jelly stem cells (hWJSCs), they have broad differentiation potential, are proliferative and available in large numbers from discarded cords thus requiring minimum ex vivo expansion. They are safe and non-tumorigenic and maintain stemness properties for prolonged periods in culture. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

161 Samples

Download data: CSV

(Submitter supplied) Bone marrow (BM) stromal cells are important in the development and maintenance of cells of the immune system. Using single cell RNA sequencing, we here explore the functional and phenotypic heterogeneity of individual transcriptomes of 1,167 murine BM mesenchymal stromal cells. These cells exhibit a tremendous heterogeneity of gene expression, which precludes the identification of defined subpopulations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: H5

(Submitter supplied) Background: Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis. Single-cell analysis tools such as FACS, FISH-FC and single-cell barcode-based sequencing can investigate cellular heterogeneity; however, they have significant limitations that impede their ability to identify and transcriptionally characterize many rare cell subpopulations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

13 Samples

Download data: JSON, TSV, TXT

(Submitter supplied) Dyskeratosis congenita (DC) is an inherited multi-system disorder, characterized by oral leukoplakia, nail dystrophy, and abnormal skin pigmentation, as well as high rates of bone marrow failure, solid tumors, and other medical problems such as osteopenia. DC and telomere biology disorders (collectively referred to as TBD here) are caused by germline mutations in telomere biology genes leading to very short telomeres and limited proliferative potential of hematopoietic stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Hypertension and persistent activation of the renin-angiotensin system (RAS) are predisposing factors for development of acute kidney injury (AKI). Although bone marrow-derived stromal cells (BMSCs) have shown therapeutic promise in treatment of AKI, the impact of pathological RAS on BMSC functionality has remained unresolved. RAS and its local components in the bone marrow are involved in several key steps of cell maturation processes. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL15084

2 Samples

Download data: TXT

(Submitter supplied) Objective: Craniofacial bone defects caused by injuries and congenital diseases are a formidable challenge to clinicians. Research has shown promise in using bone marrow mesenchymal stem cells (BM-MSCs) from limb bones for craniofacial bone regeneration; yet little is known about the potential of BM-MSCs from craniofacial bones. This study compared BM-MSCs isolated from limb and craniofacial bones in pigs, a preclinical model closely resembling humans. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16493

6 Samples

Download data: CEL, CHP

(Submitter supplied) Investigation of differential gene expression array between primary and cultured human bone marrow MSCs as adherent cells (P0 and P3) or spheres (P0 and P3)

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

19 Samples

Download data: TXT

(Submitter supplied) Mesenchymal stem cells (MSCs) are known to be heterogeneous; MSCs from different tissues show characteristic phenotypes. However, underlying molecular mechanisms of this MSC heterogeneity have not been clarified yet. In this study, to comprehensively understand transcriptome and epigenome of MSCs, we have analyzed multiple MSCs by RNA-seq and ATAC-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

36 Samples

Download data: BEDGRAPH, NARROWPEAK, TXT

(Submitter supplied) Human bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells) are manufactured using many different methods, but little is known about the spectrum of manufacturing methods used and their effects on BMSC characteristics and function. Seven centers using, and one developing, Good Manufacturing Practices (GMP) processes were surveyed as to their production methods. Among the seven centers, all used marrow aspirates as the starting material, but no two centers used the same manufacturing methods. Two to four BMSC lots from each center were compared using global gene expression. Among the twenty-four BMSC lots from the eight centers intra-center transcriptome variability was low and similar among centers. Principal component and Unsupervised Hierarchical Clustering analysis separated all the lots from five centers into five distinct clusters. BMSCs from six of the eight centers were tested for their ability to form bone and support hematopoiesis by in vivo transplantation. Those from all six centers tested formed bone, but the quantity formed was variable highly and BMSCs from only three centers supported hematopoiesis. These results show that differences in manufacturing resulted in variable BMSC characteristics including their ability to form bone and support hematopoiesis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

32 Samples

Download data: TXT