GEO DataSets

(Submitter supplied) Recent studies demonstrated that cancer stem cells (CSCs) have higher tumorigenesis properties than those of differentiated cancer cells and that transcriptional factor-SOX2 plays a vital role in maintaining the unique properties of CSCs; however, the function and underlying mechanism of SOX2 in carcinogenesis of lung cancer are still elusive. This study applied immunohistochemistry to analyze the expression of SOX2 in human lung tissues of normal individuals as well as patients with adenocarcinoma, squamous cell carcinoma, large cell and small cell carcinoma and demonstrated specific overexpression of SOX2 in all types of lung cancer tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(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.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: XLSX

(Submitter supplied) RNA-seq analysis was performed on TICs and the parental counterparts of 4 LSCC cell lines. In addition, PRKCI knock down (KD) variants of these cells were sequenced. Subsequent analysis revealed that activation of HH signaling, a known driver of the TIC phenotype, is dependent on PRKCI expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

12 Samples

Download data: TXT

(Submitter supplied) Gastric cancer is still one of the most common causes of cancer-related death worldwide, which is mainly attributable to late diagnosis and poor treatment options. Infection with H. pylori, different environmental factors and genetic alterations are known to influence the risk of developing gastric tumors. However, the molecular mechanisms involved in gastric carcinogenesis are still not fully understood, making it difficult to design targeted therapeutic approaches. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4853

Platform:

GPL6244

20 Samples

Download data: CEL

Analysis of gastric cancer (GC) cell line AZ-521 induced to express dominant-negative SOX2 (dnSOX2), a C-terminally truncated version of SOX2, for up to 24hr. Aberrant expression of specific gastric differentiation marker SOX2 has been observed in GC. Results provide insight into role of SOX2 in GC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 4 time sets

Platform:

GPL6244

Series:

GSE42937

20 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Expression profiling by array

Platforms:

GPL8186 GPL8187 GPL570

33 Samples

Download data: CEL, TXT

(Submitter supplied) To prospectively identify new oncogenes implicated in lung Squamous Cell Carcinoma pathogenesis, we investigated chromosome 3 aberrations in advanced tumours using arrayCGH. Chromosome 3 aberrations are indeed among the most frequent alterations in lung SCC and correlate with SCC patient's poor prognosis. We have precisely mapped regions of recurrent losses at 3p and gains at 3q25-qter in a series of lung SCC (GSE14859) amd moreover uncover 3q26.3-q27 high level amplifications in 20% of tumours. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8187

5 Samples

Download data: TXT

(Submitter supplied) We have identified SOX2 as a new oncogene and a likely driver of recurrent 3q26.3 amplifications in lung Squamous Cell Carcinoma. SOX2 is a crucial transcription factor implicated in Embryonic and Neural Stem Cells, that we found widely activatd in human lung SCC. This part of the study aimed at analyzing the transcriptomic consequences of SOX2 overexpression in a simple in vitro model (human lung squamous immortalized cells).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL

(Submitter supplied) To prospectively identify new oncogenes implicated in lung Squamous Cell Carcinoma pathogenesis, we investigated chromosome 3 aberrations in advanced tumours using arrayCGH. These aberrations are indeed among the most frequent aberrations in lung SCC and correlate with SCC patient's poor prognosis. We precisely map regions of recurrent losses at 3p and gains at 3q25-qter in a series of lung SCC. We moreover uncover 3q26.3-q27 high level amplifications in 20% of tumours. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8186

26 Samples

Download data: TXT

(Submitter supplied) Lineage-survival oncogenes are targeted by gene amplification in cancers arising from the tissues where these genes play a role in normal development. Here we show that the transcription factor SOX2—previously known to be mutated in hereditary human esophageal malformations, to be necessary for normal esophageal squamous development, to promote proliferation of basal tracheal cells and to co-operate in induction of pluripotent stem cells -- acts as an amplified oncogene in squamous cell carcinomas (SCC) of the lung and esophagus. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL3720

87 Samples

Download data: CEL

(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

(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

(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

(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

(Submitter supplied) This study was designed to understand the transcriptomic composition and the biological functions of cancer stem cells isolated from non-small cell lung cancer line (NSCLC) Putative lung cancer stem cells were isolated from cancer cell lines based on expression of known stem cell surface markers: CD166, CD44 and EpCAM using the Fluorescence Activated Cell Sorter (FACS).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

15 Samples

Download data: CEL, CHP

(Submitter supplied) We utilized CUT&RUN to assess the genome-wide binding of SOX2 in human small cell lung cancer cell lines.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: NARROWPEAK

(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

(Submitter supplied) To identify candidate downstream target genes of SOX2 in gastric cancer cells, we transiently expressed exogenous SOX2 in a gastric cancer cell line NUGC3 and analyzed significant changes of gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

1 Sample

Download data: TIFF, TXT

(Submitter supplied) The transcription factor SOX2 required for pluripotency, is amplified in 40% of the lung squamous cell carcinoma (LUSC) cases. However, a long-term survival analysis using TCGA cohorts of LUSC patients revealed no significant differences between high versus low SOX2 expressing cases. The treatment options for irresectable LUSC are limited to chemotherapy where carboplatin or cisplatin is given in combination with gemcitabine. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

27 Samples

Download data: TXT

(Submitter supplied) Quiescent/slowly circling tumor cells present a clinical challenge due to their ability to evade treatement. Recent studies have demonstrated that quiescent/slow circling tumor cells hijack embryonic growth arrest mechanisms and consequently resist chemotherapy. Significantly, earlier studies established that high levels of SOX2 in both fetal and tumor cells restrict cell proliferation and induce a slowly cycling state. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: BW, CSV