GEO DataSets

(Submitter supplied) We performed the integrative transcriptome analysis of human esophageal squamous cell carcinoma (ESCC) using Illumina high-throughput sequencing. A total of 187 million 38bp sequencing reads were generated containing 7 billion bases for three pairs of matched patient-derived ESCC clinical specimens and their adjacent non-tumorous tissues. By investigating the digital gene expression profiling, we found 1425 genes significantly differentially expressed and detected more than 9000 SNPs across all six samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: BAM

(Submitter supplied) Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the KYSE30 cells overexpressing an empty vector and Epist, thus identified 95 and 99 down-regulated and up-regulated genes, respectively. Expression levels of several previously reported genes implicated in cancer development and progression were altered, such as DDIT3, GATA6, UPP1, FAT3. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19615

6 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) 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) In order to understand the role of long noncoding RNAs (lncRNAs) and their interaction with coding RNAs in esophageal sqaumous cell cancer (ESCC), we performed genome-wide screening of the expression of lncRNAs and coding RNAs from primary ESCC tissue and adjacent normal tissue using Agilent SurePrint G3 Human GE 8x60K Microarray. By comparing ESCC tissues and matched normal tissues, differentially expressed lncRNAs and coding RNAs were identified and confirmed with PCR and other independent studies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL13607

8 Samples

Download data: TXT

(Submitter supplied) The aim of this study was tantamount to screen and analyze the differential expression profiles of lncRNAs in ESCC, as well as to analyze the differentially expressed lncRNAs function and related acting molecules to further understand the role of lncRNAs in the occurrence and development of ESCC.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL23178

10 Samples

Download data: CEL

(Submitter supplied) We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and esophagitis. By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21290

18 Samples

Download data: XLS

(Submitter supplied) A seven-lncRNA signature was identified in the training set, which is significantly associated with overall survival (OS) (Hazard Ratio [HR]: 3.535, 95% confidence interval [CI]: 2.113-5.915, P < 0.001) and disease-free survival (DFS) (Hazard Ratio [HR]: 2.413, 95% confidence interval [CI]: 1.573-3.703, P < 0.001). Patients in high-risk group have shorter overall survival (HR: 3.555, 95% CI: 2.195-5.757, p < 0.001) and disease-free survival (HR: 2.537, 95% CI: 1.646-3.909, p < 0.001) in the training set, and we found the same conclusion in the independent set for OS (HR 2.665, p < 0.001) and DFS (HR 2.360, p = 0.001). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL22868

222 Samples

Download data: GPR

(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) 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) Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL26963

8 Samples

Download data: TXT

(Submitter supplied) We used cDNA microarray to study the gene expression profile between the tumor and non-tumor tissue samples from patients with esophageal cancer

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

3 Samples

Download data: CEL, CHP

(Submitter supplied) Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is generally unresponsive to therapy. African Americans have an increased risk for esophageal squamous cell cancer (ESCC), the subtype that shows marked variation in geographic frequency. To identify key genes involved in ESC carcinogenesis in African Americans we conducted microarray expression profiling and found a significant dysregulation of genes encoding stress response and drug-metabolizing enzymes, mainly in NRF2 pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

14 Samples

Download data: CEL

(Submitter supplied) To further understand the expression pattern of long non-coding RNAs in early stage lung squamous cell carcinoma (SCC), we have employed the Arraystar Human LncRNA Microarray V3.0 profiling as a discovery platform to identify lncRNAs which are differentially expressed in early stage lung SCC. Three pairs of tumor tissues and adjacent normal tissues of early stage lung SCC patients are used for microarray analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16956

6 Samples

Download data: TXT

(Submitter supplied) Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using massively parallel RNA-targeting CRISPR Cas13 screens, we probed how loss of ~6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with either context-specific or broad essentiality. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

12 Samples

Download data: TXT

(Submitter supplied) In this study, we reveal insights into the biogenesis of downstream-of-gene (DoG)-containing RNAs in human cancers.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

40 Samples

Download data: BW