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) Transcriptional profiling of normal and cystinotic human renal proximal tubular epithelial cells (RPTECs) and skin fibroblasts with and without cysteine dimethyl ester (CDME). CDME- loaded RPTECs and fibroblasts did not transcriptionally mimic the cystinotic phenotype suggesting that CDME- loading is a poor surrogate in vitro model. Results highlight marked transcriptional differences between cystinotic RPTECs and fibroblasts from the same individual. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

36 Samples

Download data: XLSX

(Submitter supplied) Renal fibrosis is the common pathway in the progression of chronic kidney disease (CKD). Acyloxyacyl hydrolase (AOAH) is expressed in various phagocytes and is highly expressed in proximal tubular epithelial cells (PTECs). Research shows that AOAH plays a critical role in infections and chronic inflammatory diseases, although its role in kidney injury is unknown. Here, we found that AOAH deletion led to exacerbated kidney injury and fibrosis after folic acid (FA) administration, which was reversed by overexpression of Aoah in kidneys. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: MTX, TSV

(Submitter supplied) Macrophages are one of the major immune cell types responsible for maintaining the innate immunity of the host. They can be polarized into one of the two sub populations in vitro. M1 which is bactericidal and pro inflammatory, and M2 which is anti inflammatory and active in tissue repair. Carboxylesterases are members of the serine hydrolase superfamily. They can hydrolyze ester-containing compounds into alcohol- and carboxylic acid-containing products. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

30 Samples

Download data: TXT

(Submitter supplied) Currently there is limited knowledge of changes in genome-wide chromatin accessibility during Mycobacterium tuberculosis (Mtb) infection and whether host phosphatases such as PPM1A play a role in this process. Using combinatorial chromatin accessibility (ATAC-seq) and transcriptomics (RNA-seq) profiling of wild-type (WT), PPM1A knockout (△PPM1A) and PPM1A overexpressing (PPM1A+) macrophages, we demonstrate that Mtb infection induces global chromatin remodeling consistent with changes in gene expression signatures. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: BED, TXT

(Submitter supplied) Currently there is limited knowledge of changes in genome-wide chromatin accessibility during Mycobacterium tuberculosis (Mtb) infection and whether host phosphatases such as PPM1A play a role in this process. Using combinatorial chromatin accessibility (ATAC-seq) and transcriptomics (RNA-seq) profiling of wild-type (WT), PPM1A knockout (△PPM1A) and PPM1A overexpressing (PPM1A+) macrophages, we demonstrate that Mtb infection induces global chromatin remodeling consistent with changes in gene expression signatures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT

(Submitter supplied) To investigate transcript abundance of flavor-associated genes in fatty acid and amino acid pathways after chilling. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treatments [(A) stored at 4°C for 7 d (without chilling injury), and then transferred to room temperature (~22°C) for 1 d; (B) held at 4°C for 8 d until use (without chilling injury); (C) harvested on day 8 (8 d after the fruits of first two groups). more...

Organism:

Cucumis melo

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30269

9 Samples

Download data: XLSX

(Submitter supplied) Stimulation of the RAS-MAPK pathway activates mitogen- and stress-activated kinases (MSK) 1 and 2, which phosphorylate histone H3 at S10 (H3S10ph) or S28 (H3S28ph) (nucleosomal response) located at the regulatory regions of immediate-early genes, setting in motion a series of chromatin remodeling events that result in transcription initiation. To investigate immediate-early genes regulated by the MSK, we have completed transcriptome analyses (RNA Sequencing) of human normal fibroblast cells (CCD-1070Sk) stimulated with EGF or TPA ± H89, a potent MSK/PKA inhibitor.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL16288 GPL20301

16 Samples

Download data: CSV

(Submitter supplied) RNA-seq and RNAchIP-seq experiments were performed on MEF-derived cell lines knock-out for the expression of HP1g/CBX3 (R cell line) or recomplemented for the expression of HP1g (HPg cell line). Cells were tested under normal growth or conditions of stress (p samples) by treatment with the phorbol ester PMA. Each experiment was performed in biological triplicates.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) RNA-seq and RNAchIP-seq experiments were performed on MEF-derived cell lines knock-out for the expression of HP1g/CBX3 (R cell line) or recomplemented for the expression of HP1g (HPg cell line). Cells were tested under normal growth or conditions of stress (p samples) by treatment with the phorbol ester PMA. Each experiment was performed in biological triplicates.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Streptomyces sp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline production in these microbes. Here, we studied the production of pamamycins, macrodiolide homologues with a high activity against multi-resistant pathogenic microbes, using recombinant S. albus J1074/R2. Talc particles of micrometer size added to submerged cultures of the recombinant strain tripled pamamycin production up to 50 mg L­-1­. more...

Organism:

Streptomyces albidoflavus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28915

11 Samples

Download data: TXT

(Submitter supplied) In this study, we found that in ES cells the majority of Cdk1 substrates are localized on chromatin. Cdk1 phosphorylates a large number of proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. High levels of Cdk1 in ES cells phosphorylate and partially inactivate Dot1l, the histone H3 lysine 79 methyltransferase responsible for placing activating H3K79 marks on gene bodies. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL19057

21 Samples

Download data: BED, CSV

(Submitter supplied) Genome wide DNA methylation profiling of CD4 T cells from treated and untreated patients with multiple sclerosis. The Illumina InfiniumEPIC methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs of CD4 T cells from patients with multiple sclerosis.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

112 Samples

Download data: CSV

(Submitter supplied) This study focus a comparative toxicogenomic analysis of the effects of four herbicides (alachlor, ALA, S-metolachlor, S-MET, diuron, DIU, and MCPA-methyl ester, MCPA-ME), one insecticide (carbofuran, CAB), and one fungicide (pyrimethanil, PYR), in the model yeast Saccharomyces cerevisiae, to predict potential cytotoxic effects of these xenobiotics while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

36 Samples

Download data: CEL

(Submitter supplied) So far, we have found phorbol 12-myristate 13-acetate (PMA) induced ubiquitin specific peptidase (USP) 2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937. HL60, THP-1, and U937 undergoes differentiation into macrophage-like cells after stimulation with phorbol ester. To explore molecular function of USP2 in macrophages especially during lipopolysaccharide(LPS) response, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, CHP

(Submitter supplied) So far, we have found phorbol 12-myristate 13-acetate (PMA) induced ubiquitin specific peptidase (USP) 2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937. HL60, THP-1, and U937 undergoes differentiation into macrophage-like cells after stimulation with phorbol ester. To explore molecular function of USP2 in macrophages especially during lipopolysaccharide(LPS) response, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, CHP

(Submitter supplied) There is evidence for the on-going recurrent transfer of mitochondrial DNA (mtDNA) into the nucleus in both germ line and somatic cells. However, the outcomes associated with the transfer of mtDNA into somatic cell nuclei are poorly understood. High-resolution Chromosome Conformation Capture (HiC) techniques, which are used to identify global patterns of chromatin interactions, regularly capture physical interactions between mitochondrial and nuclear DNA (i.e. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

3 Samples

Download data: CSV

(Submitter supplied) HCMV NR-1 infection reprograms human CD34+ HPCs into long-life, NO-producing, immune suppressive Mo-MDSC-like cells at the late stage of infection We used microarray to detail the gene expression of human CD34+ HPCs and long-life, NO-producing, immune suppressive Mo-MDSC-like cells at the late stage of infection

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

2 Samples

Download data: CEL

(Submitter supplied) In this study, physical and chemical mutagenesis methods were applied to enhance lipid productivity in Chlorella vulgaris. Then, de novo RNA-seq was performed to observe lipid metabolism changes at the genome-wide level. Characterization of two mutants, UV-715 and EMS-25, showed marked increases in lipid contents, i.e., 42% and 45%, respectively. In addition, the biomass productivity of the UV-715 cells was 9% higher than that of wild-type cells. more...

Organism:

Chlorella vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23151

6 Samples

Download data: FASTA, TXT