GEO DataSets

(Submitter supplied) Characterization of gene expression changes in HuH7 HCC cells upon treatment with the Jumonji KDM inhibitor, JIB-04, GSK-J4 and SD-70 and the RAC1 inhibitor 1D-142.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: TAB

(Submitter supplied) Our RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, p53 signaling pathway, and apoptosis, and are also related to several cancers including hepatocellular carcinoma. JIB-04 also altered the expression of genes involved in various signaling pathways such as the FoxO signaling pathway, the PI3K-Akt signaling pathway, which is crucial for the proliferation and maintenance of hepatocellular carcinoma cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: GTF

(Submitter supplied) Little is known about the role of the three Jumonji C (JmjC) enzymes in Plasmodium falciparum (Pf). Here, we show that JIB-04 and other established inhibitors of mammalian JmjC histone demethylases kill asexual blood stage parasites and are even more potent at blocking gametocyte development and gamete formation. In late stage parasites, JIB-04 increased levels of trimethylated lysine residues on histones, suggesting the inhibition of P. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21298

16 Samples

Download data: TXT

(Submitter supplied) JIB-04 is an inhibitor of Jumonji histone demethylases identified through a cell based screen that measures the reactivation of an epigenetically silenced transgene. The active JIB-04 E-isomer shows selectivity for cancer vs. normal cells affecting both transcriptional patterns and cell viability in a cancer specific manner.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6884 GPL13376

18 Samples

Download data: TXT

(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:

GPL11154

22 Samples

Download data: BW

(Submitter supplied) Characterization of histone 3 lysine 4 and lysine 27 trimethylation changes upon development of taxane-platin drug resistance in NSCLC cells and evaluation of these histone modifications after treatment with Jumonji KDM inhibitors, JIB-04 and GSK-J4.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: BW

(Submitter supplied) Characterization of gene expression changes upon development of taxane-platin drug resistance in NSCLC cells and further, upon treatment of these resistant cells with the Jumonji KDM inhibitor, GSK-J4.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) While taxane-platin standard chemotherapy provides benefit in advanced and localized non-small cell lung cancer (NSCLC), the majority of patients relapse with drug resistant tumors. Mechanisms underlying NSCLC resistance to this standard doublet chemotherapy are still not fully understood, and treatment options for chemoresistant lung tumors are limited. The goals of this work were to establish new preclinical NSCLC models of resistance to taxane-platin doublet chemotherapy, identify mechanisms of resistance, and develop new rational pharmacologic approaches to target drug resistant NSCLCs.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

46 Samples

Download data: IDAT, TXT

(Submitter supplied) Cardiac hypertrophy is a potentially fatal disease characterized by increased cardiomyocyte size, and maladaptive transcriptional remodeling that leads to arrythmias and contractile failure. Transgenic mice constitutively expressing high levels of calcineurin develop extreme heart hypertrophy and generally die within a few weeks of birth. Here, we characterize the transcriptional and epigenetic pathways that are aberrant in this mouse model and establish a pharmacological approach to treating cardiac hypertrophy based on our observation that a subset of histone demethylases of the Jumonji KDM family that act on H3K4me3 or H3K9me3 are markedly increased at the protein level and show enhanced enzymatic activity in diseased hearts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

23 Samples

Download data: TXT

(Submitter supplied) Cardiac hypertrophy is a potentially fatal disease characterized by increased cardiomyocyte size, and maladaptive transcriptional remodeling that leads to arrythmias and contractile failure. Transgenic mice constitutively expressing high levels of calcineurin develop extreme heart hypertrophy and generally die within a few weeks of birth. Here, we characterize the transcriptional and epigenetic pathways that are aberrant in this mouse model and establish a pharmacological approach to treating cardiac hypertrophy based on our observation that a subset of histone demethylases of the Jumonji KDM family that act on H3K4me3 or H3K9me3 are markedly increased at the protein level and show enhanced enzymatic activity in diseased hearts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: TXT

(Submitter supplied) Cardiac hypertrophy is a potentially fatal disease characterized by increased cardiomyocyte size, and maladaptive transcriptional remodeling that leads to arrythmias and contractile failure. Transgenic mice constitutively expressing high levels of calcineurin develop extreme heart hypertrophy and generally die within a few weeks of birth. Here, we characterize the transcriptional and epigenetic pathways that are aberrant in this mouse model and establish a pharmacological approach to treating cardiac hypertrophy based on our observation that a subset of histone demethylases of the Jumonji KDM family that act on H3K4me3 or H3K9me3 are markedly increased at the protein level and show enhanced enzymatic activity in diseased hearts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) modification is implicated in the tumorigenicity of hepatocellular carcinoma (HCC). AlkB homolog 5 (ALKBH5) is one of the m6A demethylases, and it has not been well characterized in HCC. In our study we clarify the biological roles and potential mechanisms of ALKBH5 in HCC. We identify the expression profile of ALKBH5 in HCC and find that it serves as an independent prognostic factor of HCC survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: BIGWIG

(Submitter supplied) Anti-angiogenic therapy is initially effective for several solid tumors including hepatocellular carcinoma (HCC); however, they finally relapse and progress, resulting in poor prognosis. We here established in vivo drug-tolerant subclones of human HCC cells by long-term treatment with vascular endothelial growth factor receptor (VEGFR) inhibitor and serial transplantation in immunocompromised mice (total 12 months), and then compared them with the parental cells in molecular and biological features. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) Non-coding microRNAs (miRNAs) mainly regulate the expression of targeted genes by regulating mRNA degradation or repressing their protein translation. MiRNA microarray profiling was then performed on 218 human HCC tumors samples, 10 samples from adjacent cirrhotic non-tumoral tissue, 10 samples from healthy liver and 12 HCC cell lines. In this study we investigated which miRNAs were differentially expressed in HCC compared to cirrhotic non-tumoral tissue and healthy liver.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

250 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL10558

68 Samples

Download data: IDAT

(Submitter supplied) For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

34 Samples

Download data: IDAT, TXT

(Submitter supplied) There is an urgent need for developing more effective therapies for aggressive hepatocellular carcinoma (HCC). Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. The aim of this study is to identify potential therapeutic targets of SGI-110 for clinical trials.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

34 Samples

Download data: IDAT, TXT

(Submitter supplied) We performed genome-wide functional knockout screens using GECKOv2 library to identify essential growth targets in two hepatocellular carcinoma (HCC) cell lines, HCCLM3 and SNU449. We compared the gRNA present at the end of 10 passages (End Point) vs. that at Time zero in these two cell lines separately then overlap for common targets.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

5 Samples

Download data: TXT

(Submitter supplied) We used Affymetrix microarray profiling to analyze gene expression patterns in healthy donor liver as well as tumor and paired non-tumor tissue of HCC patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3921 GPL571

488 Samples

Download data: CEL, TXT

(Submitter supplied) Mouse liver tumors (T) and non tumoral adjacent livers (NT) sorted from mice knock out for Axin1 gene specifically in the hepatocytes . 3 mice of the brother hood non deleted for Axin1 were used as controls (WT) We used microarrays to determine the differential expression between tumoral and non tumoral tissue.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18802

16 Samples

Download data: CEL