GEO DataSets

(Submitter supplied) Background: Inflammation is closely related to atrial fibrillation (AF), in which macrophages play an important role as immune cells. Recent studies have shown that macrophages participate in the electron conduction in the heart, indicating that they have electrophysiological characteristics. However, whether the electrophysiology of macrophages is associated with AF remained unclear. Methods: In the present study, we investigated the electrophysiological changes in macrophages using patch-clamping after tachypacing to mimic AF. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL21273 GPL19057

51 Samples

Download data

(Submitter supplied) The transcriptional regulator Runx2 has essential roles in chondrocytes and osteoblasts, central to the coordinated development of cartilage and bone. However, the regulatory mechanisms underlying Runx2’s roles in skeletal programming are not well understood. Here, we performed an integrative analysis of Runx2–DNA binding and chromatin accessibility in vivo and identified cell type-distinct chromatin accessibility underlying Runx2 roles in osteoblasts and chondrocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL19057 GPL21273

41 Samples

Download data: BED

(Submitter supplied) A series of RNA-Seq experiment were conducted to study the transcriptome changes of olfactory sensory neurons during the critical period. We conducted RNA-seq of the olfactory epithelia at P0, P3, P7, P14, and P21 to identify the gene expression changes in the olfactory epithelia. We also performed RNA-Seq experiment of the olfactory epithelia from Kir2.1 transgenic mice at the same time points to understand the effect of neural activity deprivation on the transcriptome.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

47 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9250 GPL17021

129 Samples

Download data: H5

(Submitter supplied) The CHIP-seq methods were used to determine the binding of cyclin D1 to mouse genomic DNA. The detailed description of this dataset can be found in the publication "ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice" in Journal of Clinical Investigation (https://www.jci.org/articles/view/60256).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BAR, BED, XLS

(Submitter supplied) Lysosome-mediated macroautophagy, including lipophagy, is activated under nutrient deprivation but is repressed after feeding. We show that feeding unexpectedly activates intestinal lipophagy in a manner dependent on both the orphan nuclear receptor, small heterodimer partner (SHP/NR0B2), and the late fed-state gut hormone, fibroblast growth factor-15/19 (FGF15/19). Postprandial intestinal triglycerides (TGs) and apolipoprotein-B48 (ApoB48), the TG-rich chylomicron marker, were elevated in SHP-knockout and FGF15-knockout mice. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BW, NARROWPEAK

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

67 Samples

Download data: H5, RESULTS, TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT or Bat3 KO BMDC transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

18 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

45 Samples

Download data: RESULTS

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT or Bat3 KO BMDC transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: H5

(Submitter supplied) BCL11B and Ikaros, transcription factors essential to normal development and maturation of T cells are associated with the Mi2-beta NuRD complex in CD4+ CD8+ double-positive thymocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL11002

7 Samples

Download data: BIGBED, BW

(Submitter supplied) These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9250

2 Samples

Download data: TXT

(Submitter supplied) These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9250

2 Samples

Download data: TXT

(Submitter supplied) In this study, whole-genome ChIP-seq analysis was performed to identify Sp6 regulatory targets from postnatal mouse molars. Enriched sequence reads (peaks) from Sp6 immunoprecipitations were located predominately adjacent to transcriptional start sites. Notably enriched for Sp6 peaks were genes highly-expressed in the tooth. Bioinformatic analysis of two pools of 1400 Sp6 enriched sequences identified a consensus nine-nucleotide DNA pulldown sequence of CTg/aTAATTA from mesenchyme and the nearly identical sequence, CTa/gTAATTA, from epithelium. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BAR, BED, XLSX

(Submitter supplied) Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED, BW

(Submitter supplied) RNA (poly(A)+ fraction)was isolated from WT and Notch1-deleted mouse embryonic stem cells at the undifferetiated and differentiated (6 days; using the hanging drop model) state. Profiling of the transcritome at these two stages of differentiation using deep RNA sequencing allows identifying modulated coding and noncoding transcripts upon induction of differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

12 Samples

Download data: GTF, TXT

(Submitter supplied) This dataset is part of a study aimed to characterized and analyze the alternative splicing profiles in several models of cardiac disease and compare the changes and regulatory mechanisms to those happening during mouse heart development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: CSV, TSV

(Submitter supplied) The goal of the study was to compare gene expression of P0 wild-type and P0 Fezf2-/- cortices. Total RNAs were isolated from P0 cortices dissected from wild-type and Fezf2-/- mice (n=3 for each genotype), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA TruSeq library preparation guide.The libaries were pair-end sequenced (50nt per end). Differentially expressed genes were identified by DESEQ.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: TSV

(Submitter supplied) BRDT, a member of the BET family of double bromodomain-containing proteins, is expressed uniquely in the testis from pachytene spermatocytes through round spermatids, and is essential for spermatogenesis in the mouse. Although BRDT is known to bind to acetylated lysines in chromatin, it is not known where in the genome BRDT binds or whether the sites vary during the complex stages of differentiation in which it is expressed. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED, BEDGRAPH