GEO DataSets

(Submitter supplied) Thioredoxin Domain Containing 9 (TXNDC9) is a member of the thioredoxin family. The exact function of this protein is not known. This experiment is a transcriptiome profiling of TXNDC9 dependent RNA expression in hepatocellular carcinoma cell line HepG2. By compairing the gene expression profile of WT and TXNDC9 knockout, we identified some genes directly or indirectly regulated by TXNDC9 in hepatocellular carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(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) Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. HCC incidence is on the rise, while treatment options remain limited. Thus, a better understanding of the molecular pathways involved in HCC development has become a priority to guide future therapies. While previous studies implicated the AP-1 (Fos/Jun) transcription factor family members c-Fos and c-Jun in HCC formation, the contribution of Fos-related antigens 1 and 2 (Fra-1/2) is unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: TSV

(Submitter supplied) Hepatocellular carcinoma (HCC), the main form of liver cancer, is the sixth most common cancer and the third most frequent cause of cancer death worldwide1. The exact mechanism of HCC initiation and development is still unclear, though inflammation has been shown to play a key role in this progression. Herein, we performed a gene expression assay to screen for alterative expression of genes among normal liver tissues, HCC tissues and its paracancer tissues with hepatitis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

9 Samples

Download data: TXT

(Submitter supplied) We compared miRNA expression profiles among 5 groups of HepG2 cells treated with various concentrations (0,100,200 nM) of triptolide for 12 h or 24 h.

Organism:

Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus; Mus musculus cytomegalovirus 2; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Betapolyomavirus hominis

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

15 Samples

Download data: GPR, TXT

(Submitter supplied) Cancer cells associated with multiple survival strategies, and how cancer cells escape cell death under different conditions are still largely unknown. The Myc gene has been implicated in the pathogenesis of most types of human tumors. We show here that Eva1 (eva-1homolog A)/TMEM166 (transmembrane protein 166)/family with sequence similarity 176 (FAM176A) is upregulated by Myc/Max, however, overexpression of Eva1A induced mitotic catastrophe in hepatocellular carcinoma (HCC). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: TXT

(Submitter supplied) Here, we analyze the RNA-binding preferences of the human RDBP protein using RNAcompete.

Organism:

synthetic construct

Type:

Other

Platform:

GPL16119

1 Sample

Download data: TXT

(Submitter supplied) Global transcriptomic alterations of both coding and non-coding RNA species are a ubiquitous feature associated with human cancers including hepatocellular carcinoma (HCC). Dysregulation of RNA-binding proteins (RBPs), the key regulators of RNA processing, is one mechanism in which cancer cells select to promote tumorigenesis. We analyzed genomic alterations amongst a family of more than 800 mRNA RBPs (mRBPs) in 1,225 clinical specimens from HCC patients and found that RBPs are significantly activated through gene amplification in a subset of tumors with poor prognosis, suggesting their potential oncogenic roles in HCC progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

12 Samples

Download data: CEL

(Submitter supplied) Hepatocarcinogenesis is a multi-stage process in which precursor lesions progress into early hepatocellular carcinomas (eHCC) by sequential accumulation of multiple genetic and epigenetic alterations. To decode the molecular events during early stages of liver carcinogenesis, we performed gene expression profiling on cirrhotic (regenerative) and dysplastic nodules (DN) as well as eHCC. Although considerable heterogeneity was observed at the regenerative and dysplastic stages, clear differences were detected between DN and eHCC which included 460 differentially expressed genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1528

98 Samples

Download data: GPR

(Submitter supplied) To study the characteristics and mechanisms of Myc-induced zebrafish liver tumor, next-generation sequencing-based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up-regulated in the Myc-induced liver tumors. Cross-species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16034

8 Samples

Download data: TXT

(Submitter supplied) The MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). However, MYC is considered undruggable to date. Here, we comprehensively identify genes essential for the survival of MYC-high but not MYC-low cells by performing a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen identifies novel MYC-synthetic lethal interactions, as well as most previously identified MYC-synthetic lethal genes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

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; Other

Platforms:

GPL23479 GPL17021 GPL24247

23 Samples

Download data: TSV

(Submitter supplied) p62/SQSTM1 is a ubiquitin-binding autophagy receptor and signaling protein that accumulates in premalignant liver diseases and most hepatocellular carcinomas (HCC). Although p62 was proposed to participate in formation of benign adenomas in autophagy-deficient livers, its role in HCC initiation was not explored. Here we show that p62 is necessary and sufficient for HCC induction in mice and that its high expression level in non-tumor human liver predicts rapid HCC recurrence after curative ablation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

12 Samples

Download data: CSV

(Submitter supplied) Affymetrix Hu133 GeneCHIP Microarray data for Control and c-MYC knock-down (KD) human cancer cell lines. Data related to article 'Novel c-MYC target genes mediate differential effects on cell proliferation and migration', from D. CAPPELLEN et al., EMBO Reports Note: Samples GSM136093 and GSM136094 (Hela cell line, expt 1) were hybridized and normalized separately from the other 18 Samples. Keywords: siRNA analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2526

Platform:

GPL570

20 Samples

Download data: CEL

Analysis of breast and cervix carcinoma cell lines depleted for c-MYC by siRNA knockdown. Abnormal activation of c-MYC contributes to breast and cervix carcinogenesis. Results provide insight into the molecular basis of the developmental and oncogenic roles of MYC proteins.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 cell line, 2 other, 2 protocol sets

Platform:

GPL570

Series:

GSE5823

18 Samples

Download data: CEL

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL24676 GPL24247

19 Samples

Download data: BW, TXT

(Submitter supplied) We report the application of CUT&Tag sequencing technology for high-throughput profiling of c-Myc with core promoters of its target genes in mammalian cells. We performed CUT&Tag sequencing with antibody to total c-Myc with core promoters of its target genes in CTRLcas9 and SCARB2cas9 group. Inspection of multiple individual traces and global analyses showed that SCARB2cas9 globally reduced association of c-Myc with core promoters of its target genes.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: BW

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in liver tissue of CreAlbMYC and CreAlbScarb2F/FMYC mice by using RNA-seq. Methods: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing, using Illumina Novaseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in CTRL and PMB treatment cells by using RNA-seq. Methods: CTRL and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL24247 GPL20795 GPL24676

13 Samples

Download data: BW, MTX, TSV, TXT