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GSE46889
Mus musculus
30 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The chemokine decoy receptor D6 internalises and degrades inflammatory CC chemokines enabling resolution of inflammation. In D6 deficient mice (D6 KO), otherwise innocuous cutaneous inflammatory stimuli induce a grossly exaggerated inflammatory response that bears many similarities to human psoriasis. In the present study we have used transcriptomic approaches to define the molecular make up of this response.
Publication Title
Microarray analyses demonstrate the involvement of type I interferons in psoriasiform pathology development in D6-deficient mice.
Sample Metadata Fields
Sex, Specimen part, Treatment, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The objective of this study was to understand the gene expression changes during granulosa cell tumor development in Smad1/5/8 mutant ovaries.
Publication Title
Conditional deletion of Smad1 and Smad5 in somatic cells of male and female gonads leads to metastatic tumor development in mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 98 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Stromal-Based Signatures for the Classification of Gastric Cancer.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 78 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Increasing success is being achieved in the treatment of malignancies with stromal-targeted therapies, predominantly in anti-angiogenesis and immunotherapy, predominantly checkpoint inhibitors. Despite 15 years of clinical trials with anti-VEGF pathway inhibitors for cancer, we still find ourselves lacking reliable predictive biomarkers to select patients for anti-angiogenesis therapy. For the more recent immunotherapy agents, there are many approaches for patient selection under investigation. Notably, the predictive power of an Ad-VEGF-A164 mouse model to drive a stromal response with similarities to a wound healing response shows relevance for human cancer and was used to generate stromal signatures. We have developed gene signatures for 3 stromal states and leveraged the data from multiple large cohort bioinformatics studies of gastric cancer (TCGA, ACRG) to further understand how these relate to the dominant patient phenotypes identified by previous bioinformatics efforts. We have also designed multiplexed IHC assays that robustly represent the vascular and immune diversity in gastric cancer. Finally, we have used this methodology to arrive at a hypothesis of how angiogenesis and immunotherapy may fit into the experimental approaches for gastric cancer treatments.
Publication Title
Stromal-Based Signatures for the Classification of Gastric Cancer.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Increasing success is being achieved in the treatment of malignancies with stromal-targeted therapies, predominantly in anti-angiogenesis and immunotherapy, predominantly checkpoint inhibitors. Despite 15 years of clinical trials with anti-VEGF pathway inhibitors for cancer, we still find ourselves lacking reliable predictive biomarkers to select patients for anti-angiogenesis therapy. For the more recent immunotherapy agents, there are many approaches for patient selection under investigation.
Publication Title
Stromal-Based Signatures for the Classification of Gastric Cancer.
Sample Metadata Fields
Specimen part
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