GEO DataSets

(Submitter supplied) Investigation of whole genome gene expression level changes in Homo sapiens Esophageal squamous cell carcinoma cells KYSE30 after knock down of MTA2 gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23519

6 Samples

Download data: GPR, TXT

(Submitter supplied) Purpose：Cell division cycle associated 7 (CDCA7) is a copy number amplification gene that contributes to the metastasis and invasion of tumors, including esophageal squamous cell carcinoma (ESCC). This present study aimed at clarifying whether high expression of CDCA7 promotes the metastasis and invasion of ESCC cell lines and exploring the underlying mechanisms implicated in EMT of ESCC. Mehtod：We established KYSE150 cell lines in which target gene has been knocked down by shRNA and KYSE180 cell lines in which target gene has been ovexpressed by plasmid.We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells.Each cell has three repetions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) RNA-seq was performed on three biological replicates. Total RNA from ECA109 LV-GFP/LV-PRMT1.Differentially expressed genes were considered to be significant between groups when the P-value was <0.05 and the fold change of expression was ≥2-fold or ≤0.5-fold. By this way, the RNA-Seq data showed the differential expression genes in PRMT1 overexpression ECA109 cells compared with NC cells. Furthermore, Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) Circular RNAs (circRNAs) have been identified as a novel class of non-conding RNAs, which are stable and have covalently single-stranded loop configuration.With the improvement of RNA-sequencing and bioimofrmatics, numerous dysregulated expression of circRNAs has been identified in kinds of physiological and pathological processes, especially in tumorigenesis. To date, however, the discovery of cirtical circRNA abnormalities, as well as their functions and underlying mechanisms, in the progress of esophageal squamous cell carcinoma (ESCC), is still unknown.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21825

9 Samples

Download data: TXT

(Submitter supplied) Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

55 Samples

Download data: BED, TXT

(Submitter supplied) Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

35 Samples

Download data: TXT

(Submitter supplied) Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: BED

(Submitter supplied) Purpose: AIB1 expression is associated with disease progression in aromastase inhibitor (AI) treated patients in breast cancer. In order to identify genes aberrantly regulated by AIB1 in AI resistance, RNA-seq was carried out in endocrine resistant LetR cells and endocrine sensitive MCF7 cells +/- AIB1 under estrogen deprivation. Methods: RNA-seq was carried out in biological triplicate in MCF7 and LetR cells comparing NT (Scramble siRNA) cells versus cells depleted of AIB1 using a SMARTpool ON-TARGETplus siRNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Gene expression profiles of human BM-MSC isolated form normal donor to elucidate potential molecular network for clinical application

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) Expression of HIF-1a or Twist1 or Bmi1 in human hypopharyngeal cancer cell line FADU results in the drift of transcriptome profile from an epithelial cell-like signature to a mesenchymal stem cell-like signature.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL, CHP

(Submitter supplied) Polycomb group (PcG) proteins are essential for accurate axial body patterning during embryonic development. PcG-mediated repression is conserved in metazoans and is targeted in Drosophila by Polycomb response elements (PREs). Targeting sequences in humans have not been described. While analyzing chromatin architecture in the context of human embryonic stem cell (hESC) differentiation, we discovered a 1.8kb region between HOXD11 and HOXD12 (D11.12) that is associated with PcG proteins, is nuclease hypersensitive, and shows alteration as hESCs differentiate. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9673

10 Samples

Download data: TXT

(Submitter supplied) In this study, esophageal squamous cell carcinoma (ESCC) patients’ endoscopic biopsy tumor tissues obtained before their concomitant chemo-radiation therapy (CCRT) were used to analyze the transcriptomes by using the RNA-sequencing approach. According to retrospective study of patients’ responses to CCRT, the treatment-naive specimen can be divided into two groups (16 good CCRT response and 12 poor CCRT response). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

28 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; Expression profiling by high throughput sequencing

Platform:

GPL20301

38 Samples

Download data: BW

(Submitter supplied) Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ΔNp63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ΔNp63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

26 Samples

Download data: TXT

(Submitter supplied) Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ΔNp63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ΔNp63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

2 Samples

Download data: BEDPE

(Submitter supplied) Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ΔNp63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ΔNp63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BW

(Submitter supplied) Esophageal squamous-cell carcinoma (ESCC), one of the most prevalent and lethal malignant disease, has a complex but unknown tumor ecosystem. Here, we decipher for the first time the full compositions of ESCC tumor based on analyzing 208,659 single-cell transcriptomes in ESCC derived from 60 individuals. We identify 8 essential expression programs from malignant epithelial cells and discovered 43 cell types including 26 immune cell and 17 nonimmune stromal cell subtypes in the tumor microenvironment (TME), and also explicate the interactions between cancer cells and other cells and the interactions among different cell types in the TME. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

128 Samples

Download data: CSV, TXT

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) is the sixth leading cause of cancer death worldwide. Emerging evidence suggests that the androgen receptor (AR) is involved in ESCC tumorigenesis. However, how AR exerts its genomic functions in ESCC remains unknown. Here, by defining AR cistromes and analyzing androgen-regulated transcriptomes, we find that AR downregulates the majority of its target genes in ESCC cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

30 Samples

Download data: BEDGRAPH, BW, TXT