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SRP150005
Drosophila melanogaster
14 Downloadable Samples
NextSeq 500
Description
We characterized the Drosophila third instar eye disc using single cell RNA-seq and labelled the multiple cell populations. The results identified a novel transcriptional switch in photoreceptors relating to axonal projections. We then performed single cell RNA-seq on rbf (Rb) mutants and compared the results to the WT cell populations. This identified a specific cell population only in the Rb mutant tissue. This cell population has an upregulation of HIF1A and glycolitic genes such as Aldolase and Lactate dehydrogenase. As a result these cells produce lactate and undergo apoptosis. We also show this process to be directly regulated by E2F/Dp. The paper uncovers a novel metabolic aspect of Rb/E2F dependent apoptosis. Overall design: examining WT and Rb mutants third instar eye disc using single cell RNA-seq
Publication Title
Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
A novel mouse line was found to exhibit prominent mechanosensory deficits both behaviorally and at the primary sensory afferents, and exhibits decreased ATP release from the skin.
Publication Title
Mechanosensory and ATP Release Deficits following Keratin14-Cre-Mediated TRPA1 Deletion Despite Absence of TRPA1 in Murine Keratinocytes.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 190 Downloadable Samples
- Illumina HiSeq 2500
Description
Airway epithelial cells and macrophages differ markedly in their responses to influenza A virus (IAV) infection. To investigate transcriptional responses underlying these differences, purified subsets of type II airway epithelial cells (ATII) and alveolar macrophages (AM) recovered from the lungs of mock- or IAV-infected mice were subjected to RNA sequencing. In the absence of infection, AM predominantly expressed genes related to immunity whereas ATII expressed genes consistent with their physiological roles in the lung. Following IAV infection, AM almost exclusively activated cell-intrinsic antiviral pathways that were dependent on interferon regulatory factor (IRF)3/7 and/or type I interferon (IFN) signaling. In contrast, IAV-infected ATII activated a broader range of physiological responses, including cell-intrinsic antiviral pathways, which were both independent and dependent on IRF3/7 and/or type I IFN. These data suggest that transcriptional profiles hardwired during development could be a major determinant underlying the different responses of ATII and AM to IAV infection. Overall design: 96 samples were analyzed: (A) 4 replicates of HA+ Alveolar Macrophage (AM) and 4 replicates of CD103+ Dendritic cells (DC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ Airway epithelial cell Type II (ATII) and 4 replicates of HA+ Ciliated Cell (CC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. (B) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. (C) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8.
Publication Title
Unique Transcriptional Architecture in Airway Epithelial Cells and Macrophages Shapes Distinct Responses following Influenza Virus Infection <i>Ex Vivo</i>.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Chronic biomechanical stress elicits remodeling of the arterial wall and causes detrimental arterial stenosis and stiffening. In this context, molecular determinants controlling proliferation and stress responses of vascular smooth muscle cells (VSMCs) have been insufficiently studied. We identified the transcription factor nuclear factor of activated T-cells 5 (NFAT5) as crucial regulatory element of mechanical stress responses of VSMCs. The relevance of this observation for biomechanically induced arterial remodeling was investigated in mice upon SMC-specific knockdown of NFAT5. While blood pressure levels, vascular architecture and flow-induced collateral growth were not affected in these mice, both hypertension-mediated arterial thickening and muscularization of pulmonary arteries during pulmonary artery hypertension (PAH) were impaired. In all models, a decrease in VSMC proliferation was observed indicating that NFAT5 controls activation of VSMCs in the remodeling arterial wall. Mechanistically, mechanoactivation of VSMCs promotes nuclear translocation NFTA5c upon its phosphorylation at Y143 and dephosphorylation at S1197. As evidenced by transcriptome studies, loss of NFAT5 in mechanoactivated VSMCs impairs expression of gene products controlling cell cycle and transcription/translation. These findings identify NFAT5 as molecular determinant of VSMC responses to biomechanical stress and arterial thickening.
Publication Title
NFAT5 Isoform C Controls Biomechanical Stress Responses of Vascular Smooth Muscle Cells.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
To study the impact of the transcription factor NFAT5 on the vascular smooth muscle cell (VSMC) transcriptome, genetic ablation of floxed nfat5 in mouse aortic smooth muscle cells was achieved by transducing them with an adenoviral vector to express Cre-recombinase (Ad-Cre) under control of a CMV promoter.
Publication Title
Genetic ablation of NFAT5/TonEBP in smooth muscle cells impairs flow- and pressure-induced arterial remodeling in mice.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 86 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
The mechanisms of action of the combined targeted therapy bevacizumab erlotinib in late stage non-squamous non-small cell lung cancer was investigated by means of whole genome exon arrays.
Publication Title
24h-gene variation effect of combined bevacizumab/erlotinib in advanced non-squamous non-small cell lung cancer using exon array blood profiling.
Sample Metadata Fields
Sex, Age, Specimen part, Time
View Samples- Gallus gallus
- 12 Downloadable Samples
- Affymetrix Chicken Gene 1.1 ST Array (chigene11st)
Description
White Striping and Wooden Breast (WS/WB) are abnormalities increasingly occurring in the fillets of high breast yield and growth rate chicken hybrids. These defects lead to consistent economic losses for poultry meat industry, as affected broilers fillets present an impaired visual appearance that negatively affects consumers acceptability. Previous studies have highlighted in affected fillets a deeply damaged muscle, showing profound inflammation, fibrosis and lipidosis. The present study investigated the differentially expressed genes and pathways linked to the compositional changes observed in WS/WB breast muscles, in order to outline a more complete framework of the gene networks related to the occurrence of this complex pathological picture. The biochemical composition was performed on 20 Pectoralis major samples obtained from high breast yield and growth rate broilers (10 affected vs. 10 normal) and 12 out of the 20 samples were used for the microarray gene expression profiling (6 affected vs. 6 normal). The obtained results indicate strong changes in muscle mineral composition, coupled to an increased deposition of fat. In addition, 204 differentially expressed genes (DEG) were found: 102 up-regulated and 102 down-regulated in affected breasts. The gene expression pathways found more altered in WS/WB muscles are those related to muscle development, polysaccharide metabolic processes, proteoglycans synthesis, inflammation and calcium signaling pathway. On the whole, the findings suggest that a multifactorial and complex etiology is associated with the occurrence of WS/WB muscle abnormalities, contributing to further define the transcription patterns associated to these myopathies.
Publication Title
Detection of differentially expressed genes in broiler pectoralis major muscle affected by White Striping - Wooden Breast myopathies.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 116 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
In the current study, we used exon arrays and clinical samples from a previous trial (SAKK 19/05) to investigate the expression variations at the exon-level of 3 genes potentially playing a key role in modulating treatment response (EGFR, KRAS, VEGFA).
Publication Title
EGFR exon-level biomarkers of the response to bevacizumab/erlotinib in non-small cell lung cancer.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Peripheral whole blood-based gene expression profiling has become one of the most common strategies exploited in the development of clinically relevant biomarkers. However, the ability to identify biologically meaningful conclusions from gene expression patterns in whole blood is highly problematic. First, it is difficult to know whether or not expression patterns in whole blood capture those in primary tissues. Second, if explicit steps are not taken to accommodate the extremely elevated expression levels of globin in blood then large-scale multi-probe microarray-based studies can be severely compromised. Many studies consider the use of mouse blood as a model for human blood in addition to considering blood gene expression levels as a general surrogate for gene expression levels in other tissues. We explored the effects of globin reduction on peripheral mouse blood in the detection of genes known to be expressed in human tissues. Globin reduction resulted in 1.) a significant increase in the number of probes detected (5840 944 vs 12411 1904); 2.) increased expression for 4128 probe sets compared to non-globin reduced blood (p < .001, two-fold); 3.) improved detection of genes associated with many biological pathways and diseases; and 4.) an increased ability to detect genes expressed in 27 human tissues (p < 10-4). This study suggests that although microarray-based mouse blood gene expression studies that do not consider the effects of globin are severely compromised, globin-reduced mouse whole blood gene expression studies can be used to capture the expression profiles of genes known to contribute to various human diseases.
Publication Title
The effects of globin on microarray-based gene expression analysis of mouse blood.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 65 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence, however, indicates that sleep is necessary for normal brain function and that the need to sleep is a tightly regulated process. Surprisingly molecular mechanisms that determine the need to sleep are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need.
Publication Title
Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples