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SRP076703
Mus musculus
12 Downloadable Samples
Illumina HiScanSQ
Description
Purpose: Citron kinase (CitK) knockout mice show a severe form of primary microcephaly, associated with ataxia and lethal epilepsy. This phenotype is caused by massive apoptosis occuring during embryonic and post-natal brain development, associated with cytokinesis failure. Cerebellum is the tissue showing highest sensitivity to CitK loss. The clinical phenotype of CitK knockout mice is significantly resued by P53 inactivation. In addition, CitK/P53 double knockout brains have almost normal levels of apoptosis, but display high percentage of binucleated and multinucleated cells. The aim of this study was to analyze the gene expression changes produced in developing neural tissue by CitK loss and to determine which alterations are P53-dependent. expression changes Methods: We analyzed by RNA sequencing total RNA extracted from P4 cerebellum of mice characterized by the following genotypes: 1. CitK +/-, P53 +/- (CTRL); 2. CitK -/-, P53 +/- (CitK-KO); 3. CitK +/-, P53 -/- (P53-KO); 4. CitK -/-, P53 -/- (D-KO). Biological triplicates were analyzed per every genotype. Conclusions: The loss of CitK leads to a strong reduction of the expression of pro-neural genes and induces a P53-related pro-apoptotic gene sets. The analysis of D-KO mice reveals that most of these changes are P53-dependent, but many genes implicated in growth arrest are induced through P53-independent mechanisms. Overall design: Cerebellar mRNA profiles of 4-day old mice of CTRL, CitK-KO, P53-KO and D-KO mice were generated by deep sequencing, in triplicate, using Illumina HiScan SQ
Publication Title
ZIKA virus elicits P53 activation and genotoxic stress in human neural progenitors similar to mutations involved in severe forms of genetic microcephaly.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 101 Downloadable Samples
- Illumina HiSeq 2500
Description
The experiment aimed at determing the influence of mast cell deficiency on the transcriptome of skin-infiltrating leukocytes in K14HPV16 mice at 2month and 6month of age. Overall design: Skin-inflitrating leucocytes were FACS-purified from mast cell proficient (Mcpt5-Cre-) and mast cell deficient (Mcpt5-Cre+) K14HPV16 mice. Mast cells (CD117 high, FCeR1 high) were excluded from the sorting gate. In order to control for minimal mast cell contamination during sorting from K14HPV16 Mcpt5-Cre- skin, mast cell signature transcripts were identified by comparing transcriptomes of samples fromK14HPV16 Mcpt5-Cre- mice in which mast cells were flow cytometrically included vs excluded.
Publication Title
Although Abundant in Tumor Tissue, Mast Cells Have No Effect on Immunological Micro-milieu or Growth of HPV-Induced or Transplanted Tumors.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Mus musculus
- 38 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA seq was used to compare the expression profile of macrophages in presence and absense of mast cells. MB49 cells were injected i.d. into Mcpt5-Cre+ R26DTA animals and cre-negative littermates. Macrophages were sorted at 20 d.p.i. Overall design: Macrophage RNA profiles of MB49 TAMs (tumor-associated macrophages), harvested at 20 d.p.i. in MC-Proficient and MC-deficient animals
Publication Title
Although Abundant in Tumor Tissue, Mast Cells Have No Effect on Immunological Micro-milieu or Growth of HPV-Induced or Transplanted Tumors.
Sample Metadata Fields
Specimen part, Subject
View Samples- Schizosaccharomyces pombe
- 8 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Nitric oxide being a versatile molecule inside biological systems, from being both a cell signaling molecule to a potent stress agent, has significant effect in the transcriptional response in fission yeast.
Publication Title
Global transcriptomic profiling of Schizosaccharomyces pombe in response to nitrosative stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Sound vibration (SV) causes various developmental and physiological changes in plants. It strongly suggests the existence of sophisticated molecular mechanisms for SV perception and signaling in plants. However, the underlying molecular mechanism of SV-mediated plant responses remains elusive. Herein, we investigated the transcript changes in Arabidopsis thaliana upon five different single frequencies of SV treatment.
Publication Title
Plant acoustics: in the search of a sound mechanism for sound signaling in plants.
Sample Metadata Fields
Age, Specimen part
View Samples- Danio rerio
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit (Qiagen). Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).
Publication Title
Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The Human T-cell Leukemia Virus (HTLV)-type-I non-structural protein p30 plays an important role in virus transmission and gene regulation. p30 has been documented to inhibit the export of certain viral mRNA transcripts from the nucleus to the cytoplasm. This nuclear retainment of RNA molecules essentially results in gene silencing, where protein products are not produced.
Publication Title
Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 36 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Discriminating pathogenic bacteria from energy-harvesting commensals is key to host immunity. Using mutants defective in the enzymes of O-linked N-acetylglucosamine (O-GlcNAc) cycling, we examined the role of this nutrient-sensing pathway in the Caenorhabidits elegans innate immune response. Using whole genome transcriptional profiling, O-GlcNAc cycling mutants exhibited deregulation of unique stress- and immune-responsive genes as well as genes shared with the p38 MAPK/PMK-1 pathway. Moreover, genetic analysis showed that deletion of O-GlcNAc transferase (ogt-1) yielded animals hypersensitive to the human pathogen S. aureus but not to P. aeruginosa. Genetic interaction studies further revealed that nutrient-responsive OGT-1 acts through the conserved -catenin (BAR-1) pathway and in concert with p38 MAPK/PMK-1 to modulate the immune response to S. aureus. The participation of the nutrient sensor O-GlcNAc transferase in an immunity module conserved from C. elegans to humans reveals an unexplored nexus between nutrient availability and a pathogen-specific immune response.
Publication Title
Conserved nutrient sensor O-GlcNAc transferase is integral to C. elegans pathogen-specific immunity.
Sample Metadata Fields
Treatment
View Samples- Escherichia coli
- 14 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene with a catabolite repression mutant (referred to as crp*) alleviates diauxic effects in E. coli and enables co-utilization of glucose and other sugars. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression.
Publication Title
Transcriptional effects of CRP* expression in Escherichia coli.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Sickle cell disease is characterized by hemolysis, vaso-occlusion and ischemia reperfusion injury. These events cause endothelial dysfunction and vasculopathies in multiple systems
Publication Title
Global gene expression profiling of endothelium exposed to heme reveals an organ-specific induction of cytoprotective enzymes in sickle cell disease.
Sample Metadata Fields
Specimen part, Treatment
View Samples