GEO DataSets

(Submitter supplied) Cardiovascular disease remains a significant global health concern, yet the cardiotoxic effects of environmental chemicals are largely unexplored. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-Cardiomyocytes) are well-established as valuable high-throughput cardiotoxicity testing model based on the analysis of various beating parameters; however, additional adverse effects that may not be directly related to ion channel activity are difficult to ascertain from traditional assays. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4558 Samples

Download data: CSV

(Submitter supplied) Adipose tissue shows significant changes during aging. Here, we used single-nucleus RNA-seq to map the single-nucleus transcription profiles of mouse subcutaneous adipose tissue ( SAT ) and visceral adipose tissue ( VAT ) at a single-nucleus resolution, showing the differences in visceral and subcutaneous adipose tissue changes with aging. The mononuclear sequencing method enabled us to restore all major cell types in mouse white adipose tissue, and we characterized adipocytes, immune cells, and preadipocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: MTX, TSV

(Submitter supplied) Adipose tissue shows significant changes during aging. Here, we used single-nucleus RNA-seq to map the single-nucleus transcription profiles of mouse subcutaneous adipose tissue ( SAT ) and visceral adipose tissue ( VAT ) at a single-nucleus resolution, showing the differences in visceral and subcutaneous adipose tissue changes with aging. The mononuclear sequencing method enabled us to restore all major cell types in mouse white adipose tissue, and we characterized adipocytes, immune cells, and preadipocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) To understand cancer biology, it is crucial to unravel malignant- and microenvironmental cell states. Deconvolution of the bulk RNA profile from tumors can provide this insight, but is severely impaired by interpatient heterogeneity of the malignant cells. Bayesian statistics enables to inform RNA-deconvolution with malignant cell fraction estimates from e.g. DNA sequencing. We developed cell fraction-informed deconvolution, and evaluated this experimentally using 46 bulk RNA profiles from blood with 19 CyTOF determined cell fractions from this repository.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

48 Samples

Download data: TXT

(Submitter supplied) N,N-Diethyl-meta-toluamide (DEET) is a synthetic insect repellent invented in 1946 by the US Department of Agriculture for use by military personnel and now used worldwide as evidenced by its detection at various levels in human urine, serum, semen, and cord serum (1–5). While the neurological effects of DEET have been widely investigated (6–8), its effects on the germline and reproductive health are less understood. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

8 Samples

Download data: CSV

(Submitter supplied) The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded programme. Fruiting bodies reached highest complexity levels in the Agaricomycetes, yet, the underlying genetics is currently poorly known. In this work, we functionally characterised an unannotated gene we term snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologues of snb1 are present in almost all Agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. Snb1 mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed a multitude of differentially regulated genes and gene families that may be related to tissue differentiation and the formation of structures. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying tissue differentiation in the Agaricomycetes.

Organism:

Coprinopsis cinerea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33837

12 Samples

Download data: CSV, FASTA, GTF

(Submitter supplied) The functions of the Hsp70 genes were studied using a line of D. melanogaster with knockout of six these genes out of thirteen. Namely, effect of knockout of Hsp70 genes on negative geotaxis climbing (locomotor) speed and the ability to adapt to climbing training (0.5-1.5 h/day, 7 days/week, 19 days) were examined. Seven- and 23-day-old Hsp70– flies demonstrated a comparable reduction (2-fold) in locomotor speed and widespread changes in leg skeletal muscle transcriptome (RNA-seq), compared to w1118 flies. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22106

40 Samples

Download data: TXT

(Submitter supplied) Hepatocellular carcinoma (HCC) is the 3rd most deadly malignancy. Activated hepatic stellate cells (aHSC) give rise to cancer-associated fibroblasts in HCC and are considered a potential therapeutic target. Here we report that selective ablation of stearoyl CoA desaturase-2 (Scd2) in aHSC globally suppresses nuclear CTNNB1 and YAP1 in tumors and tumor microenvironment and prevents liver tumorigenesis in male mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

5 Samples

Download data: H5, MTX, TSV

(Submitter supplied) Hepatocellular carcinoma (HCC) is the 3rd most deadly malignancy due to limited therapeutic options. Activated hepatic stellate cells (aHSC) give rise to major cancer-associated myofibroblasts in HCC and considered a potential therapeutic target. Here we report that selective ablation of stearoyl CoA desaturase (Scd) in aHSC globally suppressed nuclear β-catenin (CTNNB1) and YAP1 in the tumor microenvironment and prevented liver tumorigenesis in mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT

(Submitter supplied) Dynamic transcriptome profiles in yak mammary gland were evaluated by sampling mammary tissue at -30, -15, 1, 15, 30, 60, 120, 180 and 240 d relative to parturition and using a bovine commercial microarray platform. Several bioinformatics tools were used to analyze the data, both as expression relative to -30 d and as expression relative to the previous time point. There were >6,000 differentially expressed transcript (DEG; FDR＜0.05; P＜0.05) throughout lactation with larger DEG observed at the onset (1 vs. more...

Organism:

Bos grunniens; Bos taurus

Type:

Expression profiling by array

Platform:

GPL11649

36 Samples

Download data: TXT

(Submitter supplied) Elderly patients suffer more brain damage in comparison with young patients from the same ischemic stroke. In that regard, it is imperative to investigate the factors responsible for decreased resistance to anti-ischemic/hypoxic injury in the aged brain. We conducted analysis of the gene expression pattern on our samples (Transient MCAO for 60 minutes established acute ischemic stroke followed by 3 days reperfusion) by the Affymetrix rat 230 2.0 chip.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

12 Samples

Download data: CEL

(Submitter supplied) Various adaptive cellular stress response pathways are critical in the pathophysiology of liver disease and drug-induced liver injury. Human-induced pluripotent stem cell (hiPSC)-derived hepatocyte-like cells (HLCs) provide a promising tool to study cellular stress response pathways, but in this context there is limited insight on how HLCs compare to primary human hepatocytes (PHH). Here, we systematically compared the activation of four different stress pathways in PHH, HepG2 liver cancer cells, hiPSCs and different stages within the differentiation towards HLCs (definitive endoderm, hepatoblast, immature hepatocytes and HLCs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

759 Samples

Download data: TXT

(Submitter supplied) Non-alcoholic fatty liver disease (NAFLD) has increased over the last decades and may evolve into hepatocellular carcinoma (HCC). As HCC is challenging to treat, knowledge on the modifia-ble risk factors for NAFLD/HCC, (e.g. hypercaloric diets rich in fructose) is essential. We used a model of diethyl nitrosamine-induced hepatocarcinogenesis to investigate the liver cancer-promoting effects of a diet supplemented with 10% liquid fructose, administered to male and female rats for 11 months. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by RT-PCR

Platform:

GPL29546

9 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

Platforms:

GPL19057 GPL21103

5 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: The goal of the study is to understand gene expression profiles of Prom1+ cells at single cell level in mouse liver cancer. Method: DEN-WAD liver from Col1a1Cre;Rosa26mTmG was perfused with collagenase. GFP+UV- cells were FACSsorted. Single cell library was constructed with 10X single gene expression v3 with 10X chromium technology. Conclusion: We identified Prom1+Afp+, Prom1+Afp-, Prom1-Afp+ gene expression profiles. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

1 Sample

Download data: MTX, TSV

(Submitter supplied) Estrogen insensitivity syndrome (EIS) arises from rare mutations in ERα resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. We used PamChip array with 154 coregulator motifs (PamGene #88101) array to compare the peptide profiles between the WT and 5 of Q375 mutants in HEK293 cells after transferred with ER alpha or Q375 mutatnts. more...

Organism:

Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL28929

42 Samples

Download data: XLSX

(Submitter supplied) Background: The AMP-activated protein kinase (AMPK) is an intracellular fuel sensor for lipid and glucose metabolism. In addition to the short-term regulation of metabolic enzymes by phosphorylation, AMPK may also exert long-term effects on the transcription of downstream genes through the regulation of transcription factors and coactivators. In this study, RNA interference (RNAi) was conducted to investigate the effects of knockdown of TcAMPKα on lipid and carbohydrate metabolism in the red flour beetle, Tribolium castaneum, and the transcriptome profiles of dsTcAMPKα-injected and dsEGFP-injected beetles under normal conditions were compared by RNA-sequencing. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18162

6 Samples

Download data: TXT

(Submitter supplied) Exposure to common environmental chemicals, including those found in personal care products has been linked to mammary cancer at high doses in animal models. Their effects at low doses at levels comparable to human exposure remain poorly understood. Using a Sprague-Dawley rat model, we investigated the effects of three prevalently used environmental chemicals – diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) – and their mixture (MIX) on the transcriptome of normal developing mammary at levels mimicking human exposure. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL17117

50 Samples

Download data: CEL

(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

Platform:

GPL17021

15 Samples

Download data: BED

(Submitter supplied) To elucidate the function of Nrf2-small Maf heterodimer, we constructed a tethered Nrf2-MafG (T-N2G) heterodimer using a flexible linker peptide and examined its function in the small Maf-deficient mouse embryonic fibroblast (MEF).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: DIFF, FPKM_TRACKING, TXT