Similar studies for GEO DataSets (Select 200106564) - GEO DataSets

Select item 2001065641.

Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [RNA-seq]

(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

Series

Accession:: GSE106564

ID:: 200106564

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2001065652.

Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung

(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

Series

Accession:: GSE106565

ID:: 200106565

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Select item 2001065633.

Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [ChIP-seq]

(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

Series

Accession:: GSE106563

ID:: 200106563

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Select item 2001064344.

TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma

(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

Series

Accession:: GSE106434

ID:: 200106434

PubMed Similar studies

Select item 2001064335.

TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma (ChIP-Seq)

(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

Series

Accession:: GSE106433

ID:: 200106433

PubMed Similar studies SRA Run Selector

Select item 2001064326.

TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma (4C-Seq)

(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

Series

Accession:: GSE106432

ID:: 200106432

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Select item 2001489207.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma

(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

Series

Accession:: GSE148920

ID:: 200148920

PubMed Similar studies SRA Run Selector

Select item 2001316618.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ChIP-Seq Drug]

(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

Series

Accession:: GSE131661

ID:: 200131661

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Select item 2001314939.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma

(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

Series

Accession:: GSE131493

ID:: 200131493

PubMed Similar studies

Select item 20013149210.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [RNA-seq]

(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

Series

Accession:: GSE131492

ID:: 200131492

Select item 20013149011.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ChIP-seq]

(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

Series

Accession:: GSE131490

ID:: 200131490

PubMed Similar studies SRA Run Selector

Select item 20013148912.

Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma [ATAC-seq]

(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

Series

Accession:: GSE131489

ID:: 200131489

PubMed Similar studies SRA Run Selector

Select item 20017892313.

SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma [4C]

(Submitter supplied) To determine whether a TP63/KLF5-regulated super-enhancer region can impact SREBF1 transcription, circularized chromosome conformation capture (4C) assays were performed. 4C assays identified complex, extensive interactions between the SREBF1 promoter and the super-enhancer region Moreover, these DNA-DNA contacts were strictly confined within the super-enhancer region, highlighting the specificity of chromatin interactions

Organism:: Homo sapiens

Type:: Other

Platform:: GPL15520
2 Samples

Download data: TXT

Series

Accession:: GSE178923

ID:: 200178923

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Select item 20014380314.

SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma

(Submitter supplied) We profiled esophageal squamous cell carcinorma (ESCC) cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. more...

Organism:: Homo sapiens

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

Platforms:: GPL10999 GPL22790
13 Samples

Download data: BW, NARROWPEAK, TXT

Series

Accession:: GSE143803

ID:: 200143803

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Select item 20004705815.

Differential gene expression by suppression of either SOX2 or TP63 in KYSE70 human esophageal squamous carcinoma cell line.

(Submitter supplied) SOX2 is a transcription factor essential for pluripotent stem cells, and development and maintenance of squamous epithelium. We previously reported SOX2 an oncogene subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs)1. Here we demonstrate in SCCs that SOX2 interacts with another master squamous transcription factor p63, and through ChIP-seq show that genomic occupancy of SOX2 overlaps with that of p63 at a large number of loci and that they cooperatively regulate gene expression including ETV4, which we find essential for SOX2-amplified SCC cell survival. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: TXT

Series

Accession:: GSE47058

ID:: 200047058

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Select item 20004683716.

SOX2 and p63 occupancy in human squamous carcinoma cell lines and embryonic stem cells.

(Submitter supplied) SOX2 is a transcription factor essential for pluripotent stem cells, and development and maintenance of squamous epithelium. We previously reported SOX2 an oncogene subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs). Here we demonstrate in SCCs that SOX2 interacts with another master squamous transcription factor p63, and through ChIP-seq show that genomic occupancy of SOX2 overlaps with that of p63 at a large number of loci and that they cooperatively regulate gene expression including ETV4, which we find essential for SOX2-amplified SCC cell survival. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
11 Samples

Download data: BED

Series

Accession:: GSE46837

ID:: 200046837

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013746117.

Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2

(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:: GPL18573
51 Samples

Download data: BED

Series

Accession:: GSE137461

ID:: 200137461

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Select item 20013746018.

Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [RNA-seq]

(Submitter supplied) Lineage-specific transcriptional regulators control differentiation states not only during normal development but also during cancer evolution. By investigating super-enhancer landscape of lung squamous cell carcinoma (LUSC), we identified a unique ‘neural’ subtype defined by Sox2 and a neural lineage factor Brn2. Robust protein-protein interaction and genomic co-occupancy of these factors indicated their transcriptional cooperation in this ‘neural’ LUSC in contrast to the cooperation of Sox2 and p63 in the classical LUSC. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
8 Samples

Download data: TXT

Series

Accession:: GSE137460

ID:: 200137460

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20013745919.

Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [ChIP-seq]

(Submitter supplied) Lineage-specific transcriptional regulators control differentiation states not only during normal development but also during cancer evolution. By investigating super-enhancer landscape of lung squamous cell carcinoma (LUSC), we identified a unique ‘neural’ subtype defined by Sox2 and a neural lineage factor Brn2. Robust protein-protein interaction and genomic co-occupancy of these factors indicated their transcriptional cooperation in this ‘neural’ LUSC in contrast to the cooperation of Sox2 and p63 in the classical LUSC. more...