GEO DataSets

(Submitter supplied) Thymic epithelial cells (TECs) are a critical functional component of the thymus’s ability to generate T cells for the adaptive immune system in vertebrates. However, no in vitro system for studying TEC function exists. Overexpressing the transcription factor FOXN1 initiates transdifferentiation of fibroblasts into TEC-like cells (iTECs) that support T cell differentiation in culture or after transplant. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

13 Samples

Download data: CSV

(Submitter supplied) Aim: Microbial colonization of the intestine in newborns is a critical event that regulates host physiology with lifelong consequences. However, there is a need to identify microbial molecules and mechanisms that play a role in this process. We aimed to elucidate the effects of flagellin, an important immunomodulatory component involved in bacterial motility, on intestinal epithelial functions. Methods: Germfree mice were colonized with synthetic bacterial communities, including a flagellated mouse gut isolate of Escherichia coli or a ΔfliC mutant thereof that lacks flagella. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: H5

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TSV

(Submitter supplied) The efficacy of costimulation blockade (CTLA4Ig/belatacept) in transplantation is reduced by an increased incidence of T cell-mediated rejection, which also persists after induction therapy with anti-thymocyte globulin (ATG). Herein, we investigate why ATG fails to prevent costimulation blockade-resistant rejection and how this barrier can be overcome. ATG did not prevent graft rejection in a murine heart transplant model of CTLA4Ig therapy and induced a pro-inflammatory cytokine environment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: TSV

(Submitter supplied) The efficacy of costimulation blockade (CTLA4Ig/belatacept) in transplantation is reduced by an increased incidence of T cell-mediated rejection, which also persists after induction therapy with anti-thymocyte globulin (ATG). Herein, we investigate why ATG fails to prevent costimulation blockade-resistant rejection and how this barrier can be overcome. ATG did not prevent graft rejection in a murine heart transplant model of CTLA4Ig therapy and induced a pro-inflammatory cytokine environment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TSV

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

Organism:

Mus musculus; Rattus norvegicus

Type:

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

4 related Platforms

65 Samples

Download data: BEDGRAPH, BW, CSV, FA, HIC, TXT

(Submitter supplied) Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved. Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved. Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: HIC

(Submitter supplied) Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved. Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. more...

Organism:

Mus musculus; Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20084 GPL19057

27 Samples

Download data: BW

(Submitter supplied) Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved. Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

15 Samples

Download data: TSV

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

23 Samples

Download data

(Submitter supplied) To interrogate transcriptomic changes in highly liver metastatic pancreatic ductal carcinoma cells as relative to their isogenic lowly metastatic cells

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

12 Samples

Download data: CSV

(Submitter supplied) Viral vectors are being used for the treatment of cancer. Yet their efficacy varies among tumors and their use poses challenges in immunosuppressed patients, underscoring the need for alternatives. We report striking antitumoral effects by a nonlytic viral vector based on attenuated lymphocytic choriomeningitis virus (r3LCMV). We show in multiple tumor models that injection of tumor-bearing mice with this novel vector results in improved tumor control and survival. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: H5

(Submitter supplied) Cell plasticity theoretically extends to all possible cell types, but naturally decreases as cells differentiate, whereas injury-repair re-engages the developmental plasticity. Here we show that the lung alveolar type 2 (AT2)-specific transcription factor (TF), CEBPA, restricts AT2 cell plasticity in the mouse lung. AT2 cells undergo transcriptional and epigenetic maturation postnatally. Without CEBPA, both neonatal and mature AT2 cells reduce the AT2 program, but only the former reactivate the SOX9 progenitor program. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

30 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Fibroblastic reticular cells (FRCs) are heterogeneous. We use single cell RNA sequencing to identify subsets of FRCs in fat-associated lymphoid clusters (FALC) in the mesenteric adipose tissue

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: TAR

(Submitter supplied) The Set7 methyltransferase regulates the expression of several genes through the methylation of histones and modulates the activity of non-histone proteins. However, the role of Set7 in cardiac remodeling and heart failure remains unknown. To address this question, wild type (WT) and Set7 knockout (KO) male mice were injected with isoproterenol (60 mg/kg) or saline subcutaneously for 14 days. WT mice injected with isoproterenol displayed a decrease in Set7 activity in the heart, although Set7 protein levels were unchanged. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: CSV

(Submitter supplied) To gain holistic of the immune landscape of lesions following infection with Mycobacterium tuberculosis, we aerosol infected C3HeB/FeJ mice with 1-3 CFU of Mtb (SA161 strain). 35 days following infection, lungs were harvested and fixed, then embedded and frozed in OCT. 10um sections were obtained, classified as necrotic or non-necrotic by visual inspection and brightfield imaging, then stained with markers delineating lesions, and subsequently processed and sampled using the nanostring GeoMX platform. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

35 Samples

Download data: CSV, DCC

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

Organism:

Danio rerio; Mus musculus

Type:

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

5 related Platforms

34 Samples

Download data: BED, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: BED, COOL, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Mus musculus; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL20828 GPL21741

14 Samples

Download data: BW, NARROWPEAK