GEO DataSets

(Submitter supplied) How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

6 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30172 GPL32159

91 Samples

Download data

(Submitter supplied) How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30172 GPL32159

65 Samples

Download data: BED, BW

(Submitter supplied) How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL30172

18 Samples

Download data: BED, BEDPE, MCOOL

(Submitter supplied) How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL30172

8 Samples

Download data: COOL

(Submitter supplied) Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell-type specific process has been a longstanding goal yet remains challenging because DNA-protein mapping methods generally study one protein at a time. To address this, we developed ChIP-DIP (ChIP Done In Parallel) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

4 related Platforms

10 Samples

Download data: BIGWIG, XLSX

(Submitter supplied) Hair loss, including alopecia, is one of the most common dermatological issues worldwide. At present, the application of fractional CO2 laser in the treatment of alopecia has been few documented, however, the results are varied between the reports. These different results may come from limited knowledge of cellular action in the laser irradiated skin. The objective of this study was to investigate the molecular and cellular mechanism of laser treatment at the affective condition for hair cycle initiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

3 Samples

Download data: TAR

(Submitter supplied) Peritoneal dialysis (PD) is a widely used kidney replacement therapy for end-stage renal failure patients. However, long-term exposure to PD fluids (PDF) can lead to peritoneal membrane (PM) damage, causing ultrafiltration failure and thus PD. Investigating the molecular mechanisms underlying this damage is crucial for identifying new therapeutic targets to mitigate peritoneal deterioration in PD patients. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

8 Samples

Download data: TXT

(Submitter supplied) CD8 T cells are potent anti-tumor mediators. We analyzed CD8 T cells from B16 tumor-draining lymphnodes from mice receiving one of three different treatments.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30172

3 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) In syngeneic solid tumor models, C5aR1 inhibition significantly enhanced the effectiveness of poly I:C, a toll-like receptor 3 (TLR3) agonist, combined with Programmed cell death protein 1 (PD-1)/Programmed cell death ligand-1 (PD-L1) blockade. In this experiment we aim to determine the effects of C5aR1 inhibition in the genes expression of Lewis Lung Cancer (LLC) tumors treated with poly I:C and PD-1 blockade combined treatment.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

24 Samples

Download data: XLSX

(Submitter supplied) Nicotinamide and pyridoxine have been identified as potent modulators of Muscle Stem cell activity. We characterized genome-wide expression profiles of NAM/PN-treated MuSC and Vehicle to verify if NAM/PN supplementation reverses MuSC dysfunction during Aging.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

8 Samples

Download data: CSV

(Submitter supplied) Objective: The early consumption of calorie-rich diet disrupts circadian rhythms and has adverse effects on memory, yet the effects of timerestricted feeding (TRF) and the underlying molecular mechanisms are unknown. Here, we set out to identify the behavioral and molecular circadian rhythms disruptions generated by juvenile obesogenic diet consumption and their restoration by TRF in male mice. Methods: Metabolic rhythms were measured by indirect calorimetry and memory performances by behavioral tasks. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

71 Samples

Download data: TXT

(Submitter supplied) The prospect of repairing the heart after a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish, amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species, the molecular mechanisms driving cardiomyocyte cell cycle re-entry remain insufficiently understood. In this study, we employed spatial transcriptomics and identified high-mobility group AT-hook 1a (Hmga1a) as being upregulated in cardiomyocytes of the injury border zone in zebrafish, but not in mice. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

7 Samples

Download data: BIGWIG

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

Organism:

Homo sapiens; Mus musculus

Type:

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

4 related Platforms

79 Samples

Download data

(Submitter supplied) Transcription factors (TFs) orchestrating lineage-development also control genes required for cellular survival. One such TF is PU.1, which is essential for myeloid development. Mice with downregulated PU.1 levels develop fatal acute myeloid leukemia (AML). However, because PU.1 is required for expression of growth factor receptors and signaling molecules, it has been unclear how PU.1-downregulated progenitors survive long enough to acquire additional alterations promoting leukemic transformation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL30172

18 Samples

Download data: FA, TSV

(Submitter supplied) Transcription factors (TFs) orchestrating lineage-development also control genes required for cellular survival. One such TF is PU.1, which is essential for myeloid development. Mice with downregulated PU.1 levels develop fatal acute myeloid leukemia (AML). However, because PU.1 is required for expression of growth factor receptors and signaling molecules, it has been unclear how PU.1-downregulated progenitors survive long enough to acquire additional alterations promoting leukemic transformation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

9 Samples

Download data: TSV

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

Organism:

Danio rerio; Mus musculus

Type:

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

4 related Platforms

42 Samples

Download data: BW, CSV, TSV

(Submitter supplied) Purpose: Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides enables the generation of spatial transcriptomes at high throughput by profiling multi-organ sections, in three dimensions by processing serial sections from one sample, and across whole human organs using spleen sections. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL30172 GPL30173

12 Samples

Download data: CSV, H5AD, MTX, PNG, TSV, TXT

(Submitter supplied) Ultraviolet B (UVB) light is a common environmental trigger that can induce flares in several autoimmune diseases. Here, we modeled photosensitivity in mice which express an autoimmune-driving isoform of Foxp3 without the second coding exon of the gene, called FoxP3ΔE2 mice. In the steady-state, FoxP3ΔE2mice generate keratinocyte-specific IgE autoantibodies and more autoreactive T follicular helper (TFH) cells that target keratinocyte-derived autoantigens that are released upon exposure to damaging doses of UVB. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

12 Samples

Download data: TXT

(Submitter supplied) Coccidioidomycosis, or Valley Fever, is a lung disease caused by inhaling Coccidioides fungi, prevalent in the Southwestern U.S., Mexico, and parts of Central and South America. Climate change is contributing to the spread of this disease. Many cases are asymptomatic, some are often misdiagnosed, and a small subset can progress to severe illness. To better understand lung responses during late Coccidioides infection, we used 10x Visium spatial transcriptomics. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL30172

2 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV