Similar studies for GEO DataSets (Select 200137461) - GEO DataSets

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Items: 20

Select item 2001374611.

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

PubMed Full text in PMC Similar studies

Select item 2001374602.

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

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Select item 2001374593.

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

Organism:: Homo sapiens

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

Platform:: GPL18573
43 Samples

Download data: BED

Series

Accession:: GSE137459

ID:: 200137459

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Select item 2001065654.

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 2001065645.

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

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Select item 2001065636.

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

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 2001225387.

Gene expression profiling of PDX-derived lung squamous carcinoma cells (TUM622) grown in 2D vs. 3D culture

(Submitter supplied) Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding tumor microenvironment (TME). Investigation of tumor cell-TME interactions could be greatly facilitated by models that mimic human disease on both the genotypic and phenotypic levels. Three dimensional (3D) cultures represent an important means to study the impact of tumor cell-TME interactions on specific aspects of neoplastic phenotypes. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
6 Samples

Download data: CEL, TXT

Series

Accession:: GSE122538

ID:: 200122538

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Select item 2000388508.

Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

(Submitter supplied) ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL15722
6 Samples

Download data: CEL

Series

Accession:: GSE38850

ID:: 200038850

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Select item 2000354969.

ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

(Submitter supplied) We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage.

Organism:: Mus musculus

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

Platforms:: GPL9250 GPL13112
30 Samples

Download data: WIG

Series

Accession:: GSE35496

ID:: 200035496

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Select item 20004705810.

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 20004683711.

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

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Select item 20004887112.

Gene expression profiles of two lung squamous cell carcinoma cell lines treated with SOX2 siRNA

(Submitter supplied) SOX2 is a transcription factor essential for self-renewal and pluripotency of embryonic stem cells. Recently SOX2 was found overexpressed in the majority of the lung squamous cell carcinoma (SQC), in which it acts as a lineage-survival oncogene. However, downstream targets/pathways of SOX2 in lung SQC cells remain to be identified. In order to identify genes/pathways likely to be downstream of SOX2, we conducted SOX2 silencing experiments in LK2 and NCI-H520 (H520 thereafter), two SOX2-abundant lung SQC cell lines and analyzed global gene transcription changes by gene expression microarray assay.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6947
4 Samples

Download data: TXT

Series

Accession:: GSE48871

ID:: 200048871

Select item 20011825213.

The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. GSE118246 (RNA-seq) GSE118245 (single cell RNA-seq by 10x Genomics) GSE118244 (Chip-Seq)

Organism:: Mus musculus

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

Platform:: GPL17021
42 Samples

Download data: BW, MTX, TSV

Series

Accession:: GSE118252

ID:: 200118252

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Select item 20011824614.

RNA sequencing of genetically engineered mouse model lung tumors and normal mouse lung.

(Submitter supplied) Genetically engineered mouse models (GEMM) of cancer are powerful tools to study multiple aspects of caner biology. We developed a novel GEMM for lung squamous cell carcinoma (LSCC) by genetically combining overexpression of Sox2 with loss of Lkb1: Rosa26LSL-Sox2-IRES-GFP;Lkb1fl/fl (SL). We compared gene expression profiles of SL lung tumors with normal mouse lung tissue, mouse lung adenocarcinoma (LADC) tumors from KrasLSL-G12D/+;Trp53fl/fl (KP), mouse LSCC tumors from Lkb1fl/fl;Ptenfl/fl (LP) model as well as Lenti-Sox2-Cre Lkb1fl/fl.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
34 Samples

Download data: TXT

Series

Accession:: GSE118246

ID:: 200118246

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Select item 20011824515.

Single-cell RNA-sequencing of tumor associated neutrophils and control peripheral blood neutrophils in a novel lung squamous cell carcinoma mouse model

(Submitter supplied) Tumor-associated neutrophils (TANs) can be conditioned to become “N2” pro-tumorigenic neutrophils in the tumor microenvironment. TANs have been shown to acquire N2 features and promote multiple aspects of tumor growth in mouse models of many cancers, including non-small cell lung cancer. We developed a novel mouse model for lung squamous cell carcinoma (LSCC): Rosa26LSL-Sox2-IRES-GFP;Nkx2-1fl/fl;Lkb1fl/fl (SNL). more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
2 Samples

Download data: MTX, TSV

Series

Accession:: GSE118245

ID:: 200118245

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011824416.

SOX2 genomic binding sites in lung squamous cell carcinoma GEMM tumor and cell lines

(Submitter supplied) SOX2 is a lineage specifier oncogene for lung squamous cell carcinoma (LSCC) and frequently amplified and overexpressed in human LSCC tumors (up to 90% of the cases). Our study demonstrated that SOX2 is a key determinant of neutrophil recruitment to tumors even in the absence of squamous histology. We generated cell lines from KrasLSL-G12D/+;Trp53fl/fl (KP) tumors that overexpress Sox2 (i.e. tumors from Lenti-Sox2-Cre infected KP mice that are validated to have Sox2 overexpression) (abbreviated as KPS) and employed chromatin immunoprecipitation sequencing (ChIP-seq) to identify genomic binding loci of SOX2 in KPS lines as well as Lkb1fl/fl;Ptenfl/fl (LP) LSCC tumors.

Organism:: Mus musculus

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

Platform:: GPL17021
6 Samples

Download data: BW

Series

Accession:: GSE118244

ID:: 200118244

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016623417.

Identification of enhancer-promoter contacts in squamous cancer cells

(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

Platforms:: GPL18573 GPL24676
54 Samples

Download data: BW, TXT

Series

Accession:: GSE166234

ID:: 200166234

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Select item 20014166618.

RNA-seq of H1299 cells in which either PRKCI or SOX2 was silenced by validated lentiviral shRNA constructs

(Submitter supplied) RNA-seq data of H1299 from NT versus PRKCI KD and NT versus SOX2 KD cells. Analysis revealed activation of oncogenic signaling pathways by PRKCI and SOX2.