Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic profiling of breast cancer stem cell spheres exposed to immune surveillence

ABSTRACT: mouse 4T1 breast cancer stem cell spheres were co-culutred with in vivo tumor antigen primed splenocytes, with in vivo tumor antigen primed splenocytes plus ex vivo reinforced activation via anti-CD3/CD28 beads or without co-culturing with splenocytes. Stem cell spheres were then collected and sunjected for gene expression analyses using RNA sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE199983 | GEO | 2022/04/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Microarray analysis of chimeric CD4+CD28null and CD4+CD28+ T-cells in humanized mice.

Project description:The major goal of this experiment was to identify the overall changes in gene expression of human CD4+CD28 null T-cells that develop after repetitive [xeno] antigen stimulation, in comparison to normal CD4+CD28+ T-cells. These cells were derived by adoptive transfer of human CD4 T-cells from a normal donor (all CD28+) into immunodeficient mice. Chimeric human CD4+CD28+ were isolated from 4 mice, and chimeric human CD4+CD28 null cells from two of these animals after expansion and T-cell differentiation in vivo. Animals were euthanized, and single cell suspensions of splenocytes derived. CD4 T-cell subpopulations were isolated by fluoresence activated cell sorting, RNA was extrated, labeled and hybridized to whole human gene expression arrays. Overall changes in the gene expression were identified using GEDI (gene expression dynamic inspector). 603 genes were found to be statistically significant (P<0.05) between the CD4+CD28+ and CD4+CD28null cells. Candidate genes were validated using qRT-PCR

2015-01-05 | E-GEOD-28484 | biostudies-arrayexpress

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shWdr5 lentivirus treated spheres )

Project description:Purpose: To determine the genome-wide effect of Wdr5 and Dpy30 suppression on acinar, duct and endocrine gene activation during pancreas spheroid differentiation Methods: We adapted an ex vivo mouse E13.5 pancreas spheroid model of growth and differentiation (Sugiyama et al., 2013) and generated RNA-sequencing data from pooled shScramble, shWdr5 and shDpy30 spheroids. Results: We identified 1,744 genes whose expression was substantially impaired and 693 genes with increased expression in shWdr5-treated spheres compared to shScramble controls. In shDpy30-treated spheres, we identified no genes with impaired expression and only 2 genes with increased expression compared to shScramble controls. Genes expressed in pancreas progenitors were largely not altered by either Wdr5 or Dpy30 suppression. However, genes expressed in the endocrine (Gcg, Ins1, Ins2 and Neurog3) and acinar (Cpa1, Cpa2 and Amy2) lineages had dramatically reduced expression in shWdr5-treated spheres, but were unaffected by Dpy30 suppression. Conclusions: These data suggest that the co-activator activity of the TrxG complexes and not their methyltransferase activity, is required for acinar and endocrine cell gene activation in an ex vivo model of pancreas development.

2019-07-12 | GSE134183 | GEO

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shDpy30 lentivirus treated spheres)

2019-07-12 | GSE134182 | GEO

miR expression profiles of human miRs in glioma spheres

2016-07-07 | GSE84106 | GEO

Expression profiling of KRas ablation surviving cells and matched Kras expressing spheres in pancreatic tumors

Project description:In this dataset, we include the expression data obtained from KRas expressing tumors, matched Kras expressing tumor spheres, surviving cells and surviving cells after KRas re-expression for 24hs Data reported here are obtained from 5 independent tumors (from 1 to 5). For each tumor, expression data for the original Tumor (in vivo bulk tumor lesion), the KRas Expressing Spheres derived from the bulk tumor, the matched surviving cells after 8 days of KRas ablation (SCs) and Surviving Cells after 24 hours of KRas re-expression are reported.

2014-06-09 | E-GEOD-58307 | biostudies-arrayexpress

Expression data of rhabdomyosarcoma cells and spheres

Project description:Rhabomyosarcoma cells can be cultured in stem cell medium over several passages and form spheres being enriched in putative cancer stem cell markers and expressing high levels of stem cell genes. In this dataset, we include RNA samples from 2 rhabdomyosarcoma cell lines and 3 different sphere passages of each cell line. 16 samples were analyzed and all sphere passages were compared to the expression level of their corresponding adherent cell line. We wanted to see an up- or downregulation of genes in the spheres to identify new potential cancer stem cell marker.

2011-04-30 | E-GEOD-26635 | biostudies-arrayexpress

miR expression profiles of human miRs in glioma spheres

Project description:In this study, we performed miRNA profiles analysis of 84, 17, 20, 83, 718, 1123, 528 and 816 glioma spheres compared to normal progenitor sample (16wf) using microarray to evaluate their potential role in regulation of the biological properties of proneural and mesenchymal glioma spheres miRNA profiling analysis of the 9 samples including 8 patient-derived samples including glioma sphere samples (84, 17, 20, 718, 816, 528, 83 and 1123), as well as one normal progenitor sample (16wf).

2016-07-07 | E-GEOD-84106 | biostudies-arrayexpress

Optimized delivery of dual co-stimulation and anti-tumor activity using parallel chimeric antigen receptors (pCARs)

Project description:Second generation (2G) chimeric antigen receptors (CARs) contain a CD28 or 41BB co-stimulatory endodomain and elicit remarkable efficacy in hematological malignancies. Third generation (3G) CARs extend this linear blueprint by fusing both co-stimulatory units in series. However, clinical impact has been muted despite compelling evidence that co-signaling by CD28 and 41BB can powerfully amplify natural immune responses. We postulate that effective dual co-stimulation requires juxta-membrane positioning of endodomain components within separate synthetic receptors. Consequently, we designed parallel (p)CARs in which a 2G (CD28+CD3) CAR is co-expressed with a 41BB-containing chimeric co-stimulatory receptor. We demonstrate that the pCAR platform optimally harnesses synergistic and tumor-dependent co-stimulation to resist T-cell exhaustion and senescence, sustaining proliferation, cytokine release, cytokine signaling and metabolic fitness upon repeated stimulation. When engineered using targeting moieties of diverse composition, affinity and specificity, pCAR T-cells consistently elicit superior anti-tumor activity both in vitro and in vivo, warranting clinical development.

2021-12-10 | GSE186557 | GEO

Gene expression in self-activating CAR-T cells with CD28 or 4-1BB costimulatory domains.

Project description:We observed self-activation of SKM-CAR-T cells which target novel mesothelioma antigen. CAR-T with CD28 costimulatory domain showed signs of exhaustion while those with 4-1BB costimulatory domain did not. Changes in the gene expression by substituting CD28 co-stimulatory domain to 4-1BB co-stimulatory domain was investigated.

2023-05-28 | GSE231443 | GEO

LNCaP prostate cancer cell line spheres (S) vs. adherent (A)

Project description:Transcriptional profile of LNCaP spheres in SCM-1% KO (stem-like cells) vs adherent cultures in RPMI-1640-10% FBS (differentiated-like cells)

2009-12-31 | GSE19704 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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