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Saccharomyces cerevisiae
43 Downloadable Samples
Illumina HiSeq 2500
Description
We studied gene expression by RNA-seq in yeast cells in various CDK1-cyclin-depleted states.
Publication Title
The CDK-APC/C Oscillator Predominantly Entrains Periodic Cell-Cycle Transcription.
Sample Metadata Fields
Disease, Cell line
View Samples- Mus musculus
- 8 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to detail the gene expression of space-flown thymic tissue and identified distinct classes of up-regulated genes during this process. We report here microarray gene expression analysis in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission, thymus lobes were extracted from space flown mice (FLT) as well as age- and sex-matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5 fold or greater change. When these data were averaged (n=4), we identified 12 genes that were significantly up- or down-regulated by at least 1.5 fold after spaceflight (p0.05). Together, these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress, glucocorticoid receptor metabolism, and T cell signaling activity. These data explain, in part, the reported systemic compromise of the immune system after exposure to the microgravity of space.
Publication Title
Microarray analysis of spaceflown murine thymus tissue reveals changes in gene expression regulating stress and glucocorticoid receptors.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 26 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Recently, we reported the development of the C57BL/6.NOD-Aec1Aec2 mouse that carries two genetic intervals derived from the NOD mouse capable of conferring Sjgrens syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice.
Publication Title
Differential gene expressions in the lacrimal gland during development and onset of keratoconjunctivitis sicca in Sjögren's syndrome (SJS)-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The C57BL/6.NOD-Aec1Aec2 mouse is a model for primary Sjgrens syndrome and was constructed by introducing two genetic intervals derived from the NOD mouse that confers Sjgrens syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice.
Publication Title
Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue's extracellular milieu precede immune responses in Sjögren's syndrome.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The transcriptome is the complete set of all RNA transcripts produced by the genome in a cell and reflects the genes that are being actively expressed. Transcriptome analysis is essential for understanding the genetic mechanism controlling the phenotype of a cell.
Publication Title
Characterization of transcriptomes of cochlear inner and outer hair cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Differential gene expression in the salivary gland during development and onset of xerostomia in Sjgrens syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.
Publication Title
Differential gene expression in the salivary gland during development and onset of xerostomia in Sjögren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 11 Downloadable Samples
- Illumina HiSeq 2500
Description
This study aims to investigate the role of microRNA-30c on hepatic and metabolic gene expression and physiology Overall design: For this experiment, we used male C57BL/6 mice. At an age of 8 weeks, we started them on Western diet for one month and then injected them with either PBS or increasing dose of Scr or miR-30c mimic (2.5, 5.0, and 7.5 mg/kg) for 6 weeks. Liver from these mice were harvested and flash frozen. RNA from the livers of these mice were extracted and RNA-seq was performed.
Publication Title
MicroRNA-30c Mimic Mitigates Hypercholesterolemia and Atherosclerosis in Mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Despite an abundance of evidence to the contrary from animal studies, large clinical trials on humans have shown that estrogen administered to post-menopausal women increases the risk of cardiovascular disease. However, timing may be everything, as estrogen is often administered immediately after ovariectomy (ovx) in animal studies, while estrogen administration in human studies occurred many years post-menopause. This study investigates the discrepancy by administering 17-estradiol (E2) in a slow-release capsule to Norway Brown rats both immediately following ovx and 9 weeks post-ovx (Late), and studying differences in gene expression between these 2 groups as compared to age-matched ovx and sham operated animals. Two different types of microarray were used to analyze the left ventricles from these groups: an Affymetrix array (2 samples/group, each sample contained total RNAs pooled from 3 rats) and an Inflammatory Cytokines and Receptors PCR array (N=4 /group). Key genes were analyzed by western blotting. Ovx without replacement led to an increase in caspase 3, caspase 9, calpain 2, MMP9, and TNF. Caspase 6, STAT3, and CD11b increased in the Late group, while TIMP2, MMP14, and collagen I 1 were decreased. MADD and fibronectin were increased in both Ovx and Late. TNF protein levels increased with Late replacement. Many of these changes were prevented by early E2 replacement. These findings suggest that increased TNF may be involved in some of the deleterious effects of delayed E2 administration seen in human studies.
Publication Title
Impact of aging vs. estrogen loss on cardiac gene expression: estrogen replacement and inflammation.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
The highly characterized Sox9-EGFP transgenic mouse model, which permits the isolation and analysis of four distinct IEC populations using fluorescence-activated cell sorting (FACS) based on differing levels of cellular EGFP intensity. These are Sox9-EGFP Low (actively cycling IESCs), Sox9-EGFP Sublow (progenitor cells), Sox9-EGFP Neg (mostly differentiated enterocytes as well as goblet cells and Paneth cells), and Sox9-EGFP High (primarily EECs). We evaluated mRNA expression profiles by next-generation high-throughput RNA-sequencing in FACS purified Sox9-Low cells from germ-free (GF) and conventionalized (CV) mice. Overall design: To assess the effect of microbiota on the intestinal epithelial stem cells population, we used four pairs of female GF Sox9-EGFP littermates. One littermate from each pair was randomly selected at 8-10 weeks of age for conventionalization. Following a two-week conventionalization, the jejunal epithelial tissue from both the CV and GF littermates were harvested and IECs were sorted by FACS. RNA was isolated from the four sorted populations from each animal, as well as from non-sorted (NS) IECs, and subject to small RNA sequencing. Additionally, Sox9-Low samples were profiled for mRNAs using mRNA-seq. Reads were aligned to the mouse genome and quantified using Salmon followed by edgeR. To avoid noise introduced by lowly expressed transcripts, we analyzed only robustly expressed transcripts defined as those with an expression of at least 10 counts per million (CPM).
Publication Title
Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples
GSE5007- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
This study compared the expression signatures of HL60 cells +/- tretinoin. This data was then used for another study showing a method for high-throughput gene expression signature analysis.
Publication Title
A method for high-throughput gene expression signature analysis.
Sample Metadata Fields
No sample metadata fields
View Samples