GEO DataSets

(Submitter supplied) Background & Aims: Lineage-specific expression of long non-coding RNAs (lncRNAs) has been observed recently. However, the underlying mechanism of such specific transcription regulation is unclear. The aim of this study is to identify squamous cell carcinoma (SCC) lineage-specific lncRNAs and to investigate the mechanisms for their expression and function. Methods: Expression characteristics and functions of four candidate SCC-specific lncRNAs were explored. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

16 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) Background & Aims: Lineage-specific expression of long non-coding RNAs (lncRNAs) has been observed recently. However, the underlying mechanism of such specific transcription regulation is unclear. The aim of this study is to identify squamous cell carcinoma (SCC) lineage-specific lncRNAs and to investigate the mechanisms for their expression and function. Methods: Expression characteristics and functions of four candidate SCC-specific lncRNAs were explored. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: BW

(Submitter supplied) In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

35 Samples

Download data: BW, TSV

(Submitter supplied) In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TSV

(Submitter supplied) In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: BW

(Submitter supplied) In esophageal squamous cell carcinoma (ESCC), the core regulatory circuitry is ill-defined and the limited clinical approaches are available currently for the treatment of ESCC. Here, using enhancer profiling and CRC programme, we generated ESCC-dependent epigenomic-transcriptional regulatory circuitry, elaborated the exquisite work model mediated by core TFs and SEs through physical interaction between enhancers and promoter, and identified the crucial target of ESCC regulatory network.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: BW

(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 GPL15207

5 Samples

Download data: CEL

(Submitter supplied) To investigate the functional role of HOTAIR in esophageal squanmous cell carcinoma (ESCC) cells, RNAi-mediated knockdown of HOTAIR and overexpression of HOTAIR were carried out using KYSE180 cells. Gene expression microarray analysis revealed that a number of reported HOTAIR target genes were regulated by HOTAIR. Moreover, gene ontology analysis revealed enrichment of genes closely related to tumorigenesis, such as cell migration, regulation of cell cycles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

3 Samples

Download data: CEL

(Submitter supplied) To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

17 Samples

Download data: BW, NARROWPEAK, TSV

(Submitter supplied) Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that the transcription factors TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. Our recent study have identified TP63 and SOX2 as super-enhancer-associated genes. However, functional consequences of their frequent co-localization at super-enhancers region remains unexplored. Here, ChIP-seq result indicated TP63 and SOX2 co-occupied peaks are significantly located the super enhancer region compare with unique of TP63 and SOX2 signaling, and combined RNA-seq analyses of different types of SCCs reveal that TP63 and SOX2 cooperatively regulate expression of the super-enhancer-associated the long non-coding RNA (lncRNA) gene, CCAT1. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TSV

(Submitter supplied) Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that the transcription factors TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. Our recent study have identified TP63 and SOX2 as super-enhancer-associated genes. However, functional consequences of their frequent co-localization at super-enhancers region remains unexplored. Here, ChIP-seq result indicated TP63 and SOX2 co-occupied peaks are significantly located the super enhancer region compare with unique of TP63 and SOX2 signaling, and combined RNA-seq analyses of different types of SCCs reveal that TP63 and SOX2 cooperatively regulate expression of the super-enhancer-associated the long non-coding RNA (lncRNA) gene, CCAT1. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) EphrinA1 overexpression-induced gene signature was significantly enriched in the cells with high expression of GMAN

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

3 Samples

Download data: TXT

(Submitter supplied) To explor the role of lncRNAs in gastric cancer progression, we performed a microarray analysis to systematically screen the differential expression of lncRNAs between six human gastric cancer tissues and their matched non-tumor tissues

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL11269

12 Samples

Download data: PAIR

(Submitter supplied) EphrinA1 silencing-induced gene signature was significantly enriched in GMAN-depleted cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

3 Samples

Download data: TXT

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC), a major type of primary esophageal cancer in developing countries, displays a very poor clinical outcome in five-year survival rate. Although long non-coding RNAs (lncRNAs) exert critical roles in cancer development, the promising therapeutic targets of ESCC-expressed lncRNAs have not been comprehensively examined and their cancer-driving roles remain largely unknown at the mechanistic level. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

46 Samples

Download data: TXT

(Submitter supplied) We constructed EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA to select differentially expressed genes and transcripts

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX