Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glioma immune microenvironment associated with malignant transformed cells Transcriptome sequencing

ABSTRACT: Ribonucleic acid sequencing (RNA-seq) of ihCTC, C12, ihDCTC, ihSTC-BM, precursor mesenchymal stem cells (MSCs) and myeloid-derived suppressor cells (MDSCs) was performed to establish a database of differentially expressed genes (DEGs).This paper intended to find the leader molecules for malignant transformation of these cells, thereby laying a foundation for the development of new molecular targeted therapy.The sequencing cell lines were established in the relevant references. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE217660 | GEO | 2025/10/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

chromosomal aberrations in prostate cancer

Project description:Prostate cancer is one of the most commonly diagnosed cancers among men in the world and the pathogenesis of prostate cancer remains poorly understood. In this study, we intended to disclose chromosomal aberrations that might be involved in tumorigenesis, using cDNA microarray-based CGH technology. Keywords: disease state analysis A total of 18 experiments were performed without replicates, using a kidney tissue as normal references. Prostate tumors and normal references were labeled with Cy5-dCTP and Cy3-dCTP, respectively.

2008-09-25 | E-GEOD-6040 | biostudies-arrayexpress

Paraoxonase 2 Serves a Proapopotic Function in Mouse and Human Cells in Response to the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-oxododecanoyl)-Homoserine Lactone.

Project description:Pseudomonas aeruginosa use quorum-sensing molecules, including N-(3-oxododecanoyl)-homoserine lactone (C12), for intercellular communication. C12 activated apoptosis in mouse embryo fibroblasts (MEF) from both wild type (WT) and Bax/Bak double knock-out mice (WT MEF and DKO MEF that were responsive to C12, DKOR MEF): nuclei fragmented; mitochondrial membrane potential (∆ψmito) depolarized; Ca2+ was released from the endoplasmic reticulum (ER), increasing cytosolic [Ca2+] (Cacyto); caspase 3/7 was activated. DKOR MEF had been isolated from a nonclonal pool of DKO MEF that were non-responsive to C12 (DKONR MEF). RNAseq analysis, qPCR and western blots showed that WT and DKOR MEF both expressed genes associated with cancer, including paraoxonase 2 (PON2), while DKONR MEF expressed little PON2. Adenovirus-mediated expression of human PON2 in DKONR MEF rendered them responsive to C12: ∆ψmito depolarized, Cacyto increased and caspase 3/7 activated. Human embryonic kidney 293T (HEK293T) cells expressed low levels of endogenous PON2, and these cells were also less responsive to C12. Overexpression of PON2, but not PON2-H114Q (no lactonase activity) in HEK293T cells caused them to become sensitive to C12. Because [C12] may reach high levels in biofilms in lungs of cystic fibrosis (CF) patients, PON2 lactonase activity may control ∆ψmito, Ca2+ release from the ER and apoptosis in CF airway epithelia. Coupled with previous data, these results also indicate that PON2 uses its lactonase activity to prevent Bax- and Bak-dependent apoptosis in response to common proapoptotic drugs like doxorubicin, staurosporine but activates Bax- and Bak-independent apoptosis in response to C12.

2015-02-14 | GSE65935 | GEO

gene profiles in prostate cancer and normal prostate tissues

Project description:Prostate cancer is one of the most commonly diagnosed cancers among men in the world and the pathogenesis of prostate cancer remains poorly understood. In this study, we intended to disclose genes that might be involved in tumorigenesis using cDNA microarray technology. Keywords: disease state analysis A total of 28 experiments were performed without replicates, using a pool of unrelated fetal tissues as common references. 25 experiments were done for prostate cancer versus common reference and 3 for normal prostate versus common reference. Prostate cancer and normal prostate samples were labeled with Cy5-dUTP. Common references were labeled with Cy3-dUTP.

2008-09-25 | E-GEOD-5957 | biostudies-arrayexpress

Single-cell gene expression profiling of oncogenically transformed small intestinal organoids upon treatment with TGF-β1

Project description:Colorectal cancer (CRC) cells infiltrating surrounding tissue commonly undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and possibly interconnected remains underexplored. Here, we used intestinal organoids with CRC driver mutations as model system to investigate the mechanistic basis of TGF‑β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype in human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF‑β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated Sox11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several, distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.

2025-05-16 | GSE278332 | GEO

Shariatpanahi2018 - Mathematical modeling of tumor-induced immunosuppression by myeloid-derived suppressor cells

Project description:This is a ODE-based mathematical model featuring equations describing the dynamics of tumor cells, cytotoxic T cells, natural killer cells, and myeloid-derived suppressor cells (MDSCs) that together describe the tumor-induced immunosuppression caused by MDSCs.

2019-09-09 | MODEL1909090003 | BioModels

Paraoxonase 2 Serves a Proapopotic Function in Mouse and Human Cells in Response to the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-oxododecanoyl)-Homoserine Lactone.

Project description:Pseudomonas aeruginosa use quorum-sensing molecules, including N-(3-oxododecanoyl)-homoserine lactone (C12), for intercellular communication. C12 activated apoptosis in mouse embryo fibroblasts (MEF) from both wild type (WT) and Bax/Bak double knock-out mice (WT MEF and DKO MEF that were responsive to C12, DKORM-BM- MEF): nuclei fragmented; mitochondrial membrane potential (M-bM-^HM-^FM-OM-^Hmito) depolarized; Ca2+M-BM- was released from the endoplasmic reticulum (ER), increasing cytosolic [Ca2+] (Cacyto); caspase 3/7 was activated. DKORM-BM- MEF had been isolated from a nonclonal pool of DKO MEF that were non-responsive to C12 (DKONRM-BM- MEF). RNAseq analysis, qPCR and western blots showed that WT and DKORM-BM- MEF both expressed genes associated with cancer, including paraoxonase 2 (PON2), while DKONRM-BM- MEF expressed little PON2. Adenovirus-mediated expression of human PON2 in DKONRM-BM- MEF rendered them responsive to C12: M-bM-^HM-^FM-OM-^HmitoM-BM- depolarized, CacytoM-BM- increased and caspase 3/7 activated. Human embryonic kidney 293T (HEK293T) cells expressed low levels of endogenous PON2, and these cells were also less responsive to C12. Overexpression of PON2, but not PON2-H114Q (no lactonase activity) in HEK293T cells caused them to become sensitive to C12. Because [C12] may reach high levels in biofilms in lungs of cystic fibrosis (CF) patients, PON2 lactonase activity may control M-bM-^HM-^FM-OM-^Hmito, Ca2+M-BM- release from the ER and apoptosis in CF airway epithelia. Coupled with previous data, these results also indicate that PON2 uses its lactonase activity to prevent Bax- and Bak-dependent apoptosis in response to common proapoptotic drugs like doxorubicin, staurosporine but activates Bax- and Bak-independent apoptosis in response to C12. Gene expression profiling of mouse embryo fibroblasts from WT and Bax/Bak double knock-out mice (C12 responsive and non-reponsive cell lines).

2015-02-14 | E-GEOD-65935 | biostudies-arrayexpress

Expression data from MDSCs at different time points during tumor progression

Project description:Myeloid-derived suppressor cells (MDSCs) are increased by tumor-derived factors and suppress anti-tumor immunity. MDSCs obtained at a late time point after tumor injection had stronger suppressive activity than MDSCs obtained at an early time point, as measured by T cell proliferation assays. To find factors in MDSCs that change during tumor growth, we analyzed gene expression profiles from MDSCs at different time points after tumor injection. We found that immune response-related genes were down-regulated, but pro-tumor function-related genes were up-regulated in both Mo-MDSCs and PMN-MDSCs at the late time point. Among differentially expressed genes, FK506 binding protein 51 (FKBP51), which is a member of the immunophilin protein family and plays a role in immunoregulation, was increased in the Mo- and PMN-MDSCs isolated from the late time points. Experiments using siRNA and a chemical inhibitor of FKBP51 revealed that FKBP51 contributes to the regulation of the suppressive function of MDSCs by increasing iNOS, ARG1, and ROS levels and enhancing NF-kappaB activity. Collectively, our data suggest that FKBP51 is a novel molecule that can be targeted to regulate the immunosuppressive function of MDSCs. To identify the factors that licensed MDSCs to be more suppressive as tumors grow, we analyzed gene expression profiles in the two subsets of MDSCs at different time points (3wks, 6wks) during tumor progression. CD11b+Ly-6C(high)Ly-6G(low) Mo-MDSCs and CD11b+Ly-6C(low)Ly-6G(high) PMN-MDSCs were sorted from pooled spleens of naÃ¯ve mice and Her-2/CT26 tumor-bearing mice. Total RNA was purified and gene expression was analyzed by the Affymetrix GeneChipÂ® Mouse Gene 1.0 ST Array.

2012-03-29 | E-GEOD-35398 | biostudies-arrayexpress

Molecular Organization of Drosophila Neuroendocrine Cells by DIMMED: Global Profiling of Pan-Neuronal DIMMED Expression Effects

Project description:To amass candidate DIMM targets in addition to Phm (Park et al., 2008a), we used genome-wide microarray profiling by over-expressing DIMM throughout the embryonic nervous system. We compared profiles from experimental (elav>dimm) and control (elav-GAL4) embryos at 22-26 hr and 28-32 hr after egg laying (AEL). The design was intended to identify transcripts consistently up-regulated shortly after the induction of DIMM; in so doing, we could circumvent the lethality that ensues in late embryonic, and/ or by early larval stages, due to pan-neuronal DIMM expression.

2011-09-06 | GSE31113 | GEO

A Cdh3 - b-Catenin - Laminin signaling axis by a subset of breast tumor leader cells controls leader cell polarization and directional collective migration

Project description:Carcinoma dissemination can occur when heterogeneous tumor and tumor stromal cells clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and interact with the microenvironment to direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system that mimics native breast tumor microenvironment, we developed 3D computational models which hypothesize that leader cells generate high protrusive forces and overcome extracellular matrix (ECM) resistance. Using single cell sequencing, we reveal leader cells are heterogeneous, and we identify and isolate a unique Cadherin-3 (Cdh3) positive leader cell subpopulation necessary and sufficient to lead migration. Cdh3 controls leader cell protrusion dynamics and local production of Laminin-332 which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration.

2022-11-25 | GSE171203 | GEO

Polistes_metricus_dominance_arrays

Project description:This experiment examined ovary gene expression differences between females in primitively eusocial Polistes metricus paper wasps. Specifically, we compared expression patterns between groups of females that differed in their reproductive dominance status. We compared dominant and subordinate foundresses, dominant and subordinate workers, and egg-laying queens. The purpose was to investigate how the social environment and dominance status affect ovary gene expression in individual females.

2014-01-15 | E-MTAB-2191 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data