GEO DataSets

(Submitter supplied) Fatty liver disease is a condition characterized by lipid accumulation in the hepatocytes and it is generally accompanied by a dyslipidemic condition characterized by low HDL levels. Being the interrelation between fatty liver disease and low HDL not clearly understood, in the present study, the impact of different apoA-I/HDL levels on the transcriptome of diet-induced fatty liver was investigated. Eight-week-old mice lacking apoA-I/HDL (DKO) and mice with physiological levels of apoA-I/HDL (DKO/hA-I) were fed either a standard rodent diet (SRD) or a Western diet (WD) for 22 weeks. Steatosis was quantified, and the hepatic transcriptome was analyzed by RNAseq. Following WD, both genotypes showed marked lipid accumulation in the liver, without relevant histological differences. The transcriptome analysis showed an upregulated expression of immune/inflammatory genes and a reduced activation of the retinoid metabolism in both WD-fed genotypes. Strong divergences in genes involved in metabolic pathways were observed only in the presence of apoA-I/HDL, where the results suggested reduced endogenous biosynthesis of cholesterol and other sterols, glutathione metabolism together with increased glucose metabolism. In conclusion, although not histologically overt, apoA-I/HDL seems to exert a substantial impact on hepatic metabolism during steatosis, that goes beyond cholesterol metabolism.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

12 Samples

Download data: CSV

(Submitter supplied) Objective: Angiotensin-II (Ang-II) drives pathological vascular wall remodeling in hypertension and abdominal aortic aneurysm (AAA). Previous studies showed that the phosphatase activity of calcineurin (Cn) mediates Ang-II-induced AAA, but the cell type involved in the action of Cn in AAA formation remained unknown. Methods: Smooth muscle cell (SMC)-specific and endothelial cell (EC)-specific Cn-deficient mice (SM-Cn-/- and EC-Cn-/- mice, respectively) were created and assessed for Ang-II-induced AAA formation and hypertension vs controls. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

40 Samples

Download data: TXT

(Submitter supplied) Chronic obstructive pulmonary disease (COPD) is associated with airway inflammation and microbiota dysbiosis. However, the function of lung microbiome alteration in early COPD remains unclear. This study is the first to characterize the lower respiratory tract microbiota in early COPD patients via bronchoalveolar lavage fluid (BALF) samples. By using full-length 16S sequencing, we found that the lung microbiome of early COPD patients had lower bacterial richness and significant compositional differences than did that of the healthy smoker controls. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

9 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11002 GPL24247

11 Samples

Download data: BED, TSV

(Submitter supplied) Alternative splicing-induced inclusion of poison exons containing in-frame stop codons is a mechanism that can be used to attenuate gene expression. Poison exon have been implicated in cancer, but how they operate within the context of normal development and physiology is poorly understood. Several splicing regulator genes, including Tra2b, contain ultra-conserved poison exons that function within regulatory loops to fine-tune their activity. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL11002

3 Samples

Download data: BED

(Submitter supplied) Recently white adipose tissues (WAT) have been shown to be able to generate heat upon cold exposure through the expression of uncoupling protein-1 (UCP1), a molecule regulating mitochondrial proton gradient. Although the role of UCP1 has been extensively investigated in adipocytes, it is currently unknown whether UCP1 in the microenvironment of WAT such as adipose-tissue macrophages (ATM) could play a role in thermogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

2 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 myocardial 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:

GPL11002

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to characterize the genetic changes that occur in muscle of mice carrying a mutant allele for STIM1 (D84G)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

8 Samples

Download data: XLSX

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL11002

4 Samples

Download data: BW, TAB

(Submitter supplied) The plant homeodomain zinc finger protein,PHF6, is a transcriptional regulator, with its germline mutations causing the X-linked intellectual disability (XLID), Börjeson-Forssman-Lehmann syndrome (BFLS).The precise mechanisms by whichPHF6regulates transcription and how its mutant forms lead to XLID remain poorly characterized. Here, we show genome-wide binding of PHF6 in the developing cortex, most of which overlap (CA)n-microsatellite repeats near genes involved in central nervous system development and neurogenesis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BED, BW

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

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17021 GPL11002

12 Samples

Download data

(Submitter supplied) We compared the expression levels of miRNAs in left ventricular heart tissue from HCM vs WT mice, using gene expression profiling data obtained from RNA-seq.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: XLSX

(Submitter supplied) We examined the dynamic changes of H3K27me3 and gene expression in neocortical neural stem cells directly isolated from various stages of embryonic brains. ChIP-seq of HMGA2 protein in the early stage of neural stem cell, and transcriptome analysis of Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/- were also performed.

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL13112 GPL11002

35 Samples

Download data: BIGWIG

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11002 GPL16417 GPL13112

25 Samples

Download data: TXT

(Submitter supplied) Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs). Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: TXT

(Submitter supplied) Using pooled shRNA libraries we performed a focused screen of 115 genes in 3D ex vivo cultures of primary murine lung tumor cells and 2D cultures of murine LKR10 cells. These screens identify Uhrf1 as gene selectively important for the 3D growth of primary lung cancer spheroids.

Organism:

Mus musculus

Type:

Other

Platform:

GPL11002

120 Samples

Download data: TSV

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array; Other

4 related Platforms

163 Samples

Download data: IDAT

(Submitter supplied) While extended loop extrusion across the entire Igh locus controls VH-DJH recombination, local regulatory sequences, such as the PAIR elements, may also activate VH gene recombination in pro-B-cells. Here we show that PAIR-associated VH8 genes contain a conserved putative regulatory element (V8E) in their downstream sequences. To investigate the function of PAIR4 and its V8.7E, we deleted all 14 PAIRs in the Igh 5’-region, which reduced distal VH gene recombination over a 100-kb distance on either side of the 890-kb deletion. more...

Organism:

Mus musculus

Type:

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

5 related Platforms

59 Samples

Download data: BW, TXT

(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

Platforms:

GPL19057 GPL11002

101 Samples

Download data

(Submitter supplied) Cancers predominantly arise from adult stem cells accumulating somatic driver mutations, but how genetic predisposition affects the penetrance of mutations in tumor initiation is not well understood. Here, we have analyzed gene expression in tumor-prone ApcMin/+ mice on highly variant C57BL/6J and PWD/Ph genetic backgrounds. We show that activation of beta-Catenin-driven and stem cell-specific gene expression in the presence of ApcMin or following APC loss is high in B6 mouse intestines, but remains moderate in intestines carrying PWD/Ph chromosome 5, suggesting that PWD/Ph variants restrict adenoma initiation by controlling stem cell homeostasis. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11002

54 Samples

Download data: CSV