GEO DataSets

(Submitter supplied) Background A large unmet therapeutic need exists in inflammatory bowel diseases (IBD). Inhibition of interleukin (IL)-6 appears to be effective, but the therapeutic benefit of a complete IL-6/IL-6R blockade is limited by profound immunosuppression. Evidence has emerged, that chronic pro-inflammatory activity of IL-6 is mainly mediated by trans-signalling via a complex of IL-6 bound to soluble IL-6R engaging the gp130 receptor without the need of membrane bound IL6R. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL21290

176 Samples

Download data: CSV, XLSX

(Submitter supplied) IgM monoclonal gammopathy of undetermined significance (IgM MGUS) is an early precursor stage of the rare lymphoma Waldenström Macroglobulinemia (WM). Although comparative gene expression studies on WM, IgM MGUS, and normal B cells identified several genes differently expressed, reliable predictors of progression from IgM MGUS to WM have not yet been identified. We performed a microarray study on CD19+ and CD138+ cells of WM vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

105 Samples

Download data: CEL

(Submitter supplied) Tenacibaculum finnmarkense is a novel Gram-negative, aerobic bacterial strain causing skin ulcers in Atlantic salmon. This is an emerging pathogen, which may cause serious problems to aquaculture. The study was designed to compare the life stages (smolt and posmolt) and to assess effects of environment (fresh and brackis water) on the course of disease and salmon responses to the pathogen.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL28080

105 Samples

Download data: TXT

(Submitter supplied) COVID-19, caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple-organ failure, but little is known about its pathophysiology. Here, we generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors. Integrated computational analysis uncovered substantial remodeling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of myofibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24268 GPL27644

188 Samples

Download data: CSV, H5, TXT

(Submitter supplied) Cancer cells function as primary architects of the tumor microenvironment. Yet, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

460 Samples

Download data: TXT

(Submitter supplied) Bipolar disorder (BD) is a severe mental disorder characterized by repeated mood swings. Although genetic factors with small effect sizes are collectively associated with the pathophysiology of BD, the underlying molecular mechanisms, especially how environmental factors affect the brain genome, remain largely unknown. We revealed neuronal cell-type-specific, pathophysiology-related DNA methylation changes in the prefrontal cortex (PFC) of BD patients, highlighting the importance of the neural epigenome for understanding BD.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

278 Samples

Download data: CEL, MAT

(Submitter supplied) Chromatin modifications have essential roles in directing nervous system development and behavior. Drosophila courtship is an ideal model for understanding the relationships between chromatin modifications, gene expression, sexual dimorphisms in neuroanatomy, and reproductive behaviors. These behaviors are largely innate and are under the control of sex determination hierarchy genes doublesex (dsx) and fruitless (fru) that encode sex-specific transcription factors. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

216 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL17275 GPL25244

250 Samples

Download data: CSV, TXT

(Submitter supplied) The Detect-seq provides an unbiased method for genome-wide identification of CBE induced off-targets inside of cells. Purpose: Cytosine base editors (CBEs) have the potential to correct human pathogenic point mutations. However, its genome-wide specificity remains poorly understood, precluding its therapeutic applications. Unbiased tools are urgently needed to comprehensively evaluate CBE off-targets at the genome-wide level. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

176 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

294 Samples

Download data: CEL, MAT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

135 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL1261 GPL16686

129 Samples

Download data: CEL

(Submitter supplied) Glial pathology has been implicated as a causal contributor to the dysfunction and death of striatal neurons that characterizes Huntington disease. In this study, we investigated mutant HTT (mHTT)-associated changes in gene expression by both mouse and human striatal astrocytes. Mouse striatal astrocytes were FACS-sorted from two distinct models, R6/2 and zQ175 mice, which respectively express exon1-only truncated or full-length HTT, while human astrocytes were generated from either hESCs expressing full-length mHTT, or fetal striatal glia transduced with exon1-only mHTT. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

111 Samples

Download data: CEL

(Submitter supplied) To investigate the transcriptional remodelling during EMT, we transfected normal murine mammary gland epithelial cells during a 4d TGFbeta treatment individually with siRNA against 46 transcription (co)factors or with 13 mature miRNA, all factors that blocked EMT in a phenotypic microscopy-based EMT screen upon RNAi . As a control, cells were transfected with siRNA/miRNA control followed by 4d TGFbeta treatment (mesenchymal control) or were left untreated (epithelial control). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

126 Samples

Download data: TXT

(Submitter supplied) To investigate the dynamics of X-chromosome reactivation, we differentiated mouse embryonic stem cells (ESCs) into neural precursor cells (NPCs) and later reprogrammed them into induced pluripotent stem cells (iPSCs). During the conversions of NPCs into iPSC, we assessed the kinetics of X-chromosome reactivation. We generated allele-specific RNA-seq datasets to assess gene reactivation dynamics, employed ATAC-seq to investigate chromatin opening dynamics and performed in situ Hi-C to explore dynamics of chromosome structure.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

116 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by array

Platforms:

GPL15520 GPL16791 GPL570

105 Samples

Download data: CEL

(Submitter supplied) Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). A collaboration between the CHDI Foundation and Dr. H.P. Nguyen (huu.nguyen-r7w@ruhr-uni-bochum.de) at Universitat Bochum focused on generating a knock-in rat model of HD that contains expanded CAG repeats inserted within the rat huntingtin gene (Hdh) in order to provide a genetic reconstruction of the human causative mutation within the rat model. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

145 Samples

Download data: TXT

(Submitter supplied) Purpose: Dietary fat-driven hyperphagia increase intestinal growth and permeability and create microbial imbalance in the gut. Over-nutrition coupled with increase in intestinal nutrient absorbance capacity then lead to nutrient overload in the liver, visceral adipose tissue followed by ectopic fat deposition with consequential lipotoxicity and inflammation. We investigated how protein quantity (10-30%) and quality (casein and whey) interact with dietary fat (20-55%) to affect these outcomes in adult mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

207 Samples

Download data: TXT

(Submitter supplied) Opioid abuse poses significant risk to individuals in the United States and epigenetic changes are a leading potential biomarker of opioid abuse. Current evidence, however, is mostly limited to candidate gene analysis in whole blood. Here, we provide Illumina HumanMethylationEPIC array data generated in dorsolateral prefrontal cortex tissue from 153 deceased invidiuals: 72 who died of acute opioid intoxication, 53 psychiatric controls, and 28 normal controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21145

153 Samples

Download data: TXT

(Submitter supplied) In the first decade of life, high-asthma risk urban children develop stable phenotypes of respiratory health versus disease that link early life environmental exposures to childhood allergic sensitization and asthma. Moreover, unique patterns of nasal gene expression demonstrate how specific molecular pathways underlie distinct respiratory phenotypes, including allergic and non-allergic asthma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

353 Samples

Download data: CSV