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GSE24826
Mus musculus
20 Downloadable Samples
Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Effective anti-viral immunity depends on the ability of infected cells or cells triggered with virus-derived nucleic acids to produce type I interferon (IFN), which activates transcription of numerous antiviral genes. However, disproportionately strong or chronic IFN expression is a common cause of inflammatory and autoimmune diseases. Here we describe an epigenetic mechanism that determines cell-type specific differences in IFN and IFN-stimulated gene expression in response to exogenous signals. We identify di-methylation of histone H3 at lysine 9 (H3K9me2) as a suppressor of IFN and IFN-inducible antiviral gene expression. We show that levels of H3K9me2 at IFN and IFN stimulated genes (ISG) correlate inversely with the scope and amplitude of IFN and ISG expression in fibroblasts and dendritic cells. Accordingly, genetic ablation or pharmacological inactivation of lysine methyltransferase G9a, which is essential for the generation of H3K9me2, resulted in phenotypic conversion of fibroblasts into highly potent IFN-producing cells and rendered these cells resistant to pathogenic RNA viruses. In summary, our studies implicate H3K9me2 and enzymes controlling its abundance as key regulators of innate antiviral immunity.
Publication Title
Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response.
Sample Metadata Fields
Treatment
View Samples- Arabidopsis thaliana
- 28 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
While pathogen-induced immunity is comparatively well characterized, far less is known about plant defense responses to arthropod herbivores. To date, most molecular-genetic studies of plant-arthropod interactions have focused on insects. However, plant-feeding (phytophagous) mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g., Lepidopteran larvae or aphids). The two-spotted spider mite, Tetranychus urticae, is among the most significant mite pests in agriculture. T. urticae is an extreme generalist that has been documented on a staggering number of plant hosts (more than 1,100), and is renowned for the rapid evolution of pesticide resistance. To understand reciprocal interactions between T. urticae and a plant host at the molecular level, we examined mite herbivory using Arabidopsis thaliana. Despite differences in feeding guilds, we found that transcriptional responses of A. thaliana to mite herbivory generally resembled those observed for insect herbivores. In particular, defense to mites was mediated by jasmonic acid (JA) biosynthesis and signaling. Further, indole glucosinolates dramatically increased mite mortality and development times. Variation in both basal and activated levels of these defense pathways might also explain differences in mite damage and feeding success between A. thaliana accessions. On the herbivore side, a diverse set of genes associated with detoxification of xenobiotics was induced upon exposure to increasing levels of in planta indole glucosinolates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.
Publication Title
Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 422 Downloadable Samples
NextSeq 500
Description
Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 221 cells from pubescent mice and 223 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 346 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads. Overall design: RNA-seq profiling was completed for 144 cells from 8 pre-puberty (2 week old) mice, 136 cells from 8 pubescent (4.7-4.9 week old) mice and 66 cells from 8 adult (10 week old) mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 311 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 75 cells from pregnant mice and 237 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 278 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 non-pregnant adult (10 week old) female mice. Epithelial cells were FACS sorted from the pregnant mice. Cells from the adult mice were FACS sorted as basal or luminal. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve 75 bp paired-end reads. Overall design: 112 basal cells and 43 luminal cells were profiled from the adult mice. 123 total epithelial cells were profiled from the pregnant mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 169 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads. Overall design: 96 basal and 90 luminal cells were profiled from 8 mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Here we determine the target gene sets controlled by PRMT1 or CSNK1a1 in maintaining the undifferentiated state of primary human keratinocytes.
Publication Title
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.
Sample Metadata Fields
Treatment
View Samples