GEO DataSets

(Submitter supplied) Uterine natural killer (uNK) cells regulate vascular changes crucial for placental function and fetal growth. The functional capacity of uNK cells is shaped by their education status. To explore the mechanisms of uNK cell education, we isolated NKG2A+ and Ly49C/I+ educated uNK cells and compared their transcriptomes to uneducated NKG2A-Ly49C/I- uNK cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

37 Samples

Download data: TXT

(Submitter supplied) Background Cisplatin-induced ototoxicity (CIO), characterized by irreversible and progressive bilateral hearing loss, is a prevalent adverse effect of cisplatin chemotherapy. Alongside clinical risk factors, genetic variants contribute to CIO and genome-wide association studies (GWAS) have highlighted the polygenicity of this adverse drug reaction. Polygenic scores (PGS), which integrate information from multiple genetic variants across the genome, offer a promising tool for the identification of individuals who are at higher risk for CIO. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34290

4 Samples

Download data: H5

(Submitter supplied) Triggering receptor expressed on myeloid cells 2 (Trem2) has been shown to be immunosuppressive in cancer and increased in obese adipose tissue. We utilized high fat and low fat diet to generate lean, obese, and weight loss mice in Trem2 wild-type (Trem2+/+) and Trem2 deficient (Trem2-/-) conditions. Once obesity and weight loss were established, mice were injected with E0771 breast cancer cells and tumors were allowed to grow for 4 weeks. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

92 Samples

Download data: CSV, MTX, RDS, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL23479 GPL16570

12 Samples

Download data: CEL, CHP

(Submitter supplied) The cAMP-response element binding protein H (CREB-H) is a transcription factor expressed in liver and intestinal tissues. It is well known for regulating many lipid and glucose metabolism genes. Our group aimed to screen for additional or potential genes that may be downstream of CREB-H transcription. To prevent inaccuracy arisen from endogenous CREB-H expression, we used CREB-H-knockout (CREB-H KO) mice for this study.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Neoadjuvant chemotherapy (NAC) is the standard treatment for muscle-invasive bladder cancer (MIBC), yet 40% of patients progress, emphasizing the need for biomarkers predictive for response or chemoresistance. Gene expression-based subtypes may serve as biomarkers, though which subtypes will respond, notably when it comes to the basal subtype, remains contentious. Patients and methods: This post hoc study analyzed 300 NAC-treated patients enrolled in the GETUG/AFU VESPER trial, with transurethral diagnostic formalin-fixed paraffin-embedded which underwent pathological review before being sequenced. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

540 Samples

Download data: TSV

(Submitter supplied) Parkinson's disease (PD) is a neurodegenerative disease characterized by bradycardia, static tremor, rigidity and postural instability. At present, the current knowledge remains inadequate for the connection between the disease severity and peripheral immune response. In the present study, using single-cell RNA sequencing (scRNA-seq), we profiled peripheral blood mononuclear cells (PBMCs) from clinical cases, including 2 early PD, 2 advance PD and 2 matched controls, representing five major immune cell subsets: T cells (CD4+, CD8+), monocytes, B cells, natural killer (NK) cells and hematopoietic stem cells (HSCs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: MTX, TSV

(Submitter supplied) Introduction Cancer is the second leading cause of death in the United States, with breast cancer being the most commonly diagnosed new cancer in women. Radiation therapy provides well-documented survival and recurrence benefits; however, it can lead to significant adverse effects, such as radiation-induced fibrosis (RIF), which can cause pain and result in poor aesthetic outcomes. The biological mechanisms underlying RIF are not entirely understood and require further investigation to identify potential intervention avenues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

42 Samples

Download data: TXT

(Submitter supplied) Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

79 Samples

Download data: DCC, PKC, TXT

(Submitter supplied) Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

119 Samples

Download data: DCC, PKC, TXT

(Submitter supplied) Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

121 Samples

Download data: DCC, PKC

(Submitter supplied) Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34810

12 Samples

Download data: RCC

(Submitter supplied) Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34809

98 Samples

Download data: RCC

(Submitter supplied) Production of PFAS has shifted from the most-studied PFAS, longer-chain perfluorinated alkyl acids, to shorter-chain or other alternative moieties including fluoroethers like HFPO-DA (“GenX chemicals”), Nafion Byproducts, and the PFOx homologous series that includes PFO4DA and PFO5DoA. In contaminated study areas, the fluoroethers PFO4DA and PFO5DoA, although detected at relatively low levels in surface water, have been detected in serum and/or tissues with high frequency in humans, wildlife including fish and alligators, and pets including horses. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

111 Samples

Download data: TSV

(Submitter supplied) Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. more...

Organism:

Bubalus bubalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL31047

6 Samples

Download data: CSV

(Submitter supplied) The use of aqueous film-forming foams (AFFF) at fire-training areas (FTAs) has introduced into ground- and surface waters a complex mixture of per- and poly-fluorinated alkyl substances (PFAS). The toxicity of environmental PFAS mixtures to wildlife is not well understood and presents a knowledge gap that limits accurate risk assessment. To evaluate reproductive biomarker responses to complex environmental PFAS mixtures, we conducted a series of on-site experiments using flow-through mobile laboratories exposing fish to groundwater impacted by a legacy FTA and an adjacent reference site A 60K fathead minnow microarray was used to quantify gene expression patterns in the testis and liver of fish exposed to water from Fire Training Area 1 and 2 relative to a reference site.

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

31 Samples

Download data: TXT

(Submitter supplied) The use of aqueous film-forming foams (AFFF) at fire-training areas (FTAs) has introduced into ground- and surface waters a complex mixture of per- and poly-fluorinated alkyl substances (PFAS). The toxicity of environmental PFAS mixtures to wildlife is not well understood and presents a knowledge gap that limits accurate risk assessment. To evaluate reproductive biomarker responses to complex environmental PFAS mixtures, we conducted a series of on-site experiments using flow-through mobile laboratories exposing fish to groundwater impacted by a legacy FTA and an adjacent reference site A 60K fathead minnow microarray was used to quantify gene expression patterns in the testis and liver of fish exposed to water from Fire Training Area 1 and 2 relative to a reference site.

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

22 Samples

Download data: TXT

(Submitter supplied) Extracellular vesicles (EVs) hold the potential for elucidating the pathogenesis and serving as biomarkers of amyotrophic lateral sclerosis (ALS). Notably, the comparative and longitudinal alterations in the protein profiles of EVs in serum (sEVs) and CSF (cEVs) of sporadic ALS (SALS) patients remain unexplored. This study sought to reveal such changes by collecting serum and CSF at fixed intervals from 10 controls and 20 SALS patients participating in the Ropinirole Hydrochloride Remedy for Amyotrophic Lateral Sclerosis trial. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for dense graph recovery. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

270 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases. Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease. To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE). more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array

Platforms:

GPL570 GPL6804

180 Samples

Download data: CEL, CHP