Filters
Technology
Platform
SRP142312
Mus musculus
74 Downloadable Samples
NextSeq 500
Description
Single-cell expression profiling is a rich resource of cellular heterogeneity. While profiling every sample under study is advantageous, such workflow is time consuming and costly. We devised CPM - a deconvolution algorithm in which cellular heterogeneity is inferred from bulk expression data based on pre-existing collection of single-cell RNA-seq profiles. We applied CPM to investigate individual variation in heterogeneity of murine lung cells during in vivo influenza virus infection, revealing that the relations between cell quantities and clinical outcomes varies in a gradual manner along the cellular activation process. Validation experiments confirmed these gradual changes along the cellular activation trajectory. Additional analysis suggests that clinical outcomes relate to the rate of cell activation at the early stages of this process. These findings demonstrate the utility of CPM as a mapping deconvolution tool at single-cell resolution, and highlight the importance of such fine cell landscape for understanding diversity of clinical outcomes. Overall design: Lungs gene expression of Collaborative Cross mice taken 48h after the infection with either the influenza virus or PBS.
Publication Title
Cell composition analysis of bulk genomics using single-cell data.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 150 Downloadable Samples
Illumina mouseRef-8 v1.1 expression beadchip
Description
Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending lifespan
Publication Title
Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending life span.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Differences in the inherent properties of undifferentiated fat cell progenitors may contribute to the biological specificity of the abdominal subcutaneous (Sc) and visceral omental (V) fat depots. In this study, the biological characteristics of three distinct subpopulations of adipose tissue-derived stem cells (ASC), i.e. ASCSVF, ASCBottom and ASCCeiling isolated from Sc and V adipose tissue biopsies of non-obese subjects, were investigated. Genome-wide differential gene expression analysis followed by quantitative RT-PCR and analysis of cytokines in the ASC-derived conditioned medium were performed. By analysis of 28,869 annotated genes, 1,019 genes resulted differentially expressed between Sc-ASC and V-ASC. Within the Sc-ASC and V-ASC populations, 546 and 1,222, respectively, were the genes differentially expressed among ASCSVF, ASCBottom and ASCCeiling. A far more striking difference was found when the hierarchical clusters analysis was performed comparing each Sc-ASC with its own homologous V-ASC subset. mRNA levels of HoxA5, Tbx15, PI16, PITPNC1, FABP5, IL-6, IL-8, MCP-1, VEGF, MMP3, TFPI2, and ANXA10 were significantly different between Sc-ASC and V-ASC. Of the 27 cytokines measured, 14 (IL-2, IL-4, IL-5 IL-7, IL-9, IL-10, IL12, IL13, MIP1-, MIP1-, PDGF-, FGFbasic, GM-CSF, IP-10) were not released, whereas 13 were expressed (IL-1beta, IL-1ra, IL-15, IL-17, G-CSF, IFN, RANTES, TNF-, Eotaxin, IL-8, MCP-1, VEGF, IL-6), and of these, MCP-1, Eotaxin, IL-1ra, FGFbasic, IL-6, IL-8, G-CSF, and VEGF were significantly different among ASCSVF, ASCCeiling and ASCBottom of the two adipose tissue depots. These results demonstrate the existence of genetically and functionally heterogeneous fat-derived ASC populations, which may add to the complexity and specificity of Sc and V adipose tissue in humans.
Publication Title
Differences in gene expression and cytokine release profiles highlight the heterogeneity of distinct subsets of adipose tissue-derived stem cells in the subcutaneous and visceral adipose tissue in humans.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose.
Publication Title
Functional dissection of sugar signals affecting gene expression in Arabidopsis thaliana.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 52 Downloadable Samples
- Illumina HiSeq 1000
Description
We report differences in mRNA gene expression in rectal biopsies from MSM compared to controls and for MSM timed with episodes of CRAI. Overall design: Rectal biopsies were obtained from MSM at two study timepoints: 1. after who abstaining from CRAI for >72 hours and 2.after engaing in CRAI within the last 24 hours. Rectal biopsies were also obtained from men who never engaged in AI.
Publication Title
Short Communication: Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV Negative Men Who Have Sex with Men Engaging in Condomless Receptive Anal Intercourse.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Analysis of T-cells lacking the proprotein convertase furin. Proprotein convertases promote the proteolytic maturation of proproteins. Furin is induced in activated T-cells. Results provide insight into the function of furin in T-cells.
Publication Title
Proprotein convertase FURIN regulates T cell receptor-induced transactivation.
Sample Metadata Fields
Age, Treatment
View Samples- Arabidopsis thaliana
- 26 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptomic analysis of gene expression during the differentiation of cell suspension cultures into tracheary elements using the biological system published by Pesquet et al., Current Biology (2010): tracheary element differentiation was triggered by externally supplying hormone-free habituated cell suspension cultures of Arabidopsis thaliana Col-0 with auxin, cytokinin and epibrassinolides; RNA samples extracted from 3 independent time-courses every 12h from 0h to 4 days were analyzed using ATH1 Arabidopsis Affymetrix micro-array
Publication Title
Proteomic Analysis of Microtubule Interacting Proteins over the Course of Xylem Tracheary Element Formation in Arabidopsis.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 17 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
The basic defect of IgA nephropathy (IgAN) lies within peripheral blood mononuclear cells rather than local kidney abnormalities. Previously we showed an altered gene expression in monocytes compared to B and T cells isolated from IgAN patients (Kidney Int, 2010), thus our aim here was to study this subset more closely at genome-wide level.
Publication Title
Altered monocyte expression and expansion of non-classical monocyte subset in IgA nephropathy patients.
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We studied adipose tissue from wild type mice, kinin B1 receptor knockout mice (B1KO), and B1KO mice with rescued expression of kinin B1 receptor selectively in fat.
Publication Title
Kinin B1 and B2 receptor deficiency protects against obesity induced by a high-fat diet and improves glucose tolerance in mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Cyclin D1 is an important cell cycle regulator but in cancer its overexpression also increases cellular migration mediated by p27KIP1 stabilization and RhoA inhibition. Recently, a common polymorphism at the exon 4-intron 4 boundary of the human cyclin D1 gene within a splice donor region was associated with an altered risk of developing cancer. Altered RNA splicing caused by this polymorphism gives rise to a variant cyclin D1 isoform termed cyclin D1b, which has the same N-terminus as the canonical cyclin D1a isoform but a distinct C-terminus. Analysis was performed of mouse cyclin D1 knockout 3T3 cells infected with splice variants of cyclin D1. 3T3 cells transduced with retroviral vectors expressing each cyclin D1 isoform were processed for expression analysis.
Publication Title
Alternate cyclin D1 mRNA splicing modulates p27KIP1 binding and cell migration.
Sample Metadata Fields
No sample metadata fields
View Samples