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Homo sapiens, Rattus norvegicus
10 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Synovial and bone marrow mesenchymal stem cells after intradiscally injection show regenerative effects of nucleus pulposus.
Publication Title
Intradiscal transplantation of synovial mesenchymal stem cells prevents intervertebral disc degeneration through suppression of matrix metalloproteinase-related genes in nucleus pulposus cells in rabbits.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
One of strategies to regenerate cartilage defect is transplantation of mesenchymal stem cells (MSCs). Improvements of therapeutic potential of MSCs are needed to achieve successful cartilage regeneration by transplantation of a limited number of cells. Aggregated culture is a popular method in ES and iPS cells to maintain or enhance their potentials. Here we investigated gene expression profile of aggregated MSCs. 621 genes were up-regulated and 409 genes were down-regulated more than 5-fold in MSC-aggregates compared with the number in MSCs in a monolayer culture. The most up-regulated gene was BMP2, which is one of the genes involved in chondrogenesis. Anti-inflammatory genes were also up-regulated in MSC-aggregates. The microarray data for selected genes were confirmed by real-time PCR.
Publication Title
Properties and usefulness of aggregates of synovial mesenchymal stem cells as a source for cartilage regeneration.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hsp90 is critical for regulation of the phenotype and functional activity of human T lymphocytes and natural killer (NK) cells.
Publication Title
Heat shock protein 90 is critical for regulation of phenotype and functional activity of human T lymphocytes and NK cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples
GSE10934- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The sclera maintains and protects the eye ball, which receives visual inputs. The aim of this study is to identify characteristics of the human sclera as one of the connective tissues derived from the neural crest and mesoderm. We have here demonstrated microarray data of cultured human scleral cells.
Publication Title
Human sclera maintains common characteristics with cartilage throughout evolution.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Heme ameliorates dextran sodium sulfate-induced colitis through providing intestinal macrophages with noninflammatory profiles.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
In murine large intestinal lamina propria, CX3CR1high resident Mfs possess anti-inflammatory properties and thereby support intestinal homeostasis. Unlike other tissue-resident Ms, transcription factors that regulate differentiation and function of CX3CR1high Ms in the large intestine are poorly understood. Thus, to identify transcription factors specifically expressed in CX3CR1high Ms among large intestinal lamina propria innate myeloid cells, we comprehensively analyzed the genes expression profiles in CX3CR1high Ms, CX3CR1- CD11b+ CD11c+ cells, CD11b- CD11chigh DCs, and CD11b+CD11c- cells.
Publication Title
Heme ameliorates dextran sodium sulfate-induced colitis through providing intestinal macrophages with noninflammatory profiles.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
Illumina HiSeq 2500
Description
To determine the functions of Spi-C in innate immune responses, we investigated the overall gene expression patterns in M-CSF-BMDMFs prepared from Spicflox/flox and Lyz2-cre; Spicflox/flox mice. M-CSF-BMDMFs were stimulated with or without LPS following heme treatment and used for RNA-seq analysis. Overall design: Control and Spic–/– BMDMF pretreated with 40 µM hemin for 18 h were stimulated with (designated 'CNT_4' and 'cKO_4', respectively) or without (designated 'CNT_0' and 'cKO_0', respectively) 100 ng/ml LPS for 4 h.
Publication Title
Heme ameliorates dextran sodium sulfate-induced colitis through providing intestinal macrophages with noninflammatory profiles.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 25 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Room temperature whole blood mRNA stabilization procedures, such as the PAX gene system, are critical for the application of transcriptional analysis to population-based clinical studies. Global transcriptome analysis of whole blood RNA using microarrays has proven to be challenging due to the high abundance of globin transcripts that constitute 70% of whole blood mRNA in the blood. This is a particular problem in patients with sickle-cell disease, secondary to the high abundance of globin-expressing nucleated red blood cells and reticulocytes in the circulation . In order to more accurately measure the steady state whole blood transcriptome in sickle-cell patients, we evaluated the efficacy of reducing globin transcripts in PAXgene stabilized RNA samples for genome-wide transcriptome analyses using oligonucleotide arrays. We demonstrate here by both microarrays and Q-PCR that the globin mRNA depletion method resulted in 55-65 fold reduction in globin transcripts in whole blood collected from healthy volunteers and sickle-cell disease patients. This led to an improvement in microarray data quality with increased detection rate of expressed genes and improved overlap with the expression signatures of isolated peripheral blood mononuclear (PBMC) preparations. The differentially modulated genes from the globin depleted samples had a higher correlation coefficient to the 112 genes identified to be significantly altered in our previous study on sickle-cell disease using PBMC preparations. Additionally, the analysis of differences between the whole blood transcriptome and PBMC transcriptome reveals important erythrocyte genes that participate in sickle-cell pathogenesis and compensation. The combination of globin mRNA reduction after whole-blood RNA stabilization represents a robust clinical research methodology for the discovery of biomarkers for hematologic diseases and in multicenter clinical trials investigating a wide range of nonhematologic disorders where fractionation of cell types is impracticable.
Publication Title
Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 49 Downloadable Samples
- NextSeq 500
Description
Reprogram-Seq leverages organ-specific cell atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Overall design: Focusing on the cardiac system, we performed Reprogram-Seq on P0 mouse heart cells to generate a reference transcriptomic map. Based on the reference map, we selected TF candidates and tests 1000s of TF cocktails for direct lineage conversion by scRNA-Seq.
Publication Title
Rational Reprogramming of Cellular States by Combinatorial Perturbation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 36 Downloadable Samples
- NextSeq 500
Description
Reprogram-Seq leverages organ-specific cell atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Overall design: Focusing on the cardiac system, we performed Reprogram-Seq on P0 mouse heart cells to generate a reference transcriptomic map. Based on the reference map, we selected TF candidates and tests 1000s of TF cocktails for direct lineage conversion by scRNA-Seq.
Publication Title
Rational Reprogramming of Cellular States by Combinatorial Perturbation.
Sample Metadata Fields
Specimen part, Subject
View Samples