GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

32 Samples

Download data: MTX, TSV

(Submitter supplied) Tumor-bearing mammary fat pads from MMTV-PyMT mice were digested with 2mg/mL Collagenase A and 2U/mL Dnase.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate the gene expression profile of different cancer associated fibroblasts (CAF) subpopulations, we harvested tumors and sorted 4 CAF populations from 3 FVB background 10-week-old MMTV-PyMT mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TSV

(Submitter supplied) The dynamics of immune reprogramming in the breast cancer lung metastastic niche remains incomplete. We used MULTI-seq (McGinnis, Patterson, et al., Nature Methods, 2019) to perform multiplexed single-cell RNA-sequencing analysis of cryopreserved lung immune cells isolated from PyMT mice, freshly-isolated lung immune cells isolated from PyMT mice, and cryopreserved lung immune cells isolated from 4T1 tumor-bearing mice from the onset of primary tumorigenesis through the formation of macrometastatic lesions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

38 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Loss of muscle mass is a pathological driver in both chronic illness and aging. We have discovered that skeletal muscle specific thrombospondin-1 (Thbs1) transgenic mice have profound muscle atrophy with age-dependent decreases in exercise capacity and premature lethality. Here, we compared the transcriptional profiles of skeletal muscle from control non-transgenic mice with those overexpressing Thbs1 in order to elucidate the transcriptional changes underlying the observed effects on skeletal muscle mass. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

4 Samples

Download data: XLSX

(Submitter supplied) Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TSV

(Submitter supplied) Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse normal and tumor samples, and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in pre-malignant tumor cells expressing markers of lineage plasticity and drug resistance. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

28 Samples

Download data: RDS

(Submitter supplied) We identify gene profiling of astrocytes by Cytokine or PBS stimulation in vivo.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

32 Samples

Download data: TAGALIGN, TSV

(Submitter supplied) Relapse in T-cell acute lymphoblastic leukemia (T-ALL) may signify the persistence of leukemia-initiating cells (L-ICs). Ectopic TAL1/LMO expression defines the largest subset of T-ALL, but its role in leukemic transformation and its impact on relapse-driving L-ICs remain poorly understood. In TAL1/LMO mouse models, double negative-3 (DN3; CD4−CD8−CD25+CD44−) thymic progenitors harbored L-ICs. However, only a subset of DN3 leukemic cells exhibited L-IC activity, and studies linking L-ICs and chemotolerance are needed. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: MTX, TSV

(Submitter supplied) Lung cancer is the leading cause of cancer-related deaths in the world, and non-small cell lung cancer (NSCLC) is the most common subset. Although immune checkpoint inhibitors have improved outcomes in a subset of NSCLC patients, these effects are usually not durable. Thus, a more complete understanding of how immune niches within the tumor microenvironment (TME) promote NSCLC progression will allow us to build upon these advances. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

21 Samples

Download data: TXT

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL26624

2 Samples

Download data: BED, BW

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL26624 GPL21273

36 Samples

Download data: BW, MTX, TSV

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: BED, BW

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: BW, XLSX

(Submitter supplied) Disruption of Cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting deposition of H3K9 trimethylation (H3K9me3). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: BW, XLSX

(Submitter supplied) Mammary tumors of parental and aggressive variants of an ErbB2+ breast cancer mouse model that differs in the degree to which is is experiencing oxidative stress as a result of forced expression of an oxidative stress inducer called p66ShcA.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TSV

(Submitter supplied) We used in situ vaccination with autologous dendritic cell secreting CCL21, in combination with immune checkpoint inhibitor, anti-PD-1, to treat oncogene-driven non-small cell lung cancer in a murine model. The single cell transcriptome of the treated cancer tissues were measured.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: MTX, TSV

(Submitter supplied) Despite advances in genetics over the last two decades, relating genetic variants to behavior remains a fundamental challenge. Particularly in mice, progress is frustrated by the low resolution of genetic mapping, and consequently by the thousands of candidate causal variants that must be screened. To assess the utility of DNA methylation marks in discovering causative variants we examined their relationship to genetic variation by generating genome-wide, base-pair resolution maps of multiple cell types from the hippocampus of eight fully sequenced inbred strains of Mus musculus. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TSV