Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

57 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of human ex vivo cultivated urothelial carcinoma samples transduced with a trivalent adenoviral vector (Im02) for activation of the immune tumor microenvironment.

ABSTRACT: The trivalent adenoviral vector Im02 encodes the cDNAs for human 4-1BBL, IL-12 and IL-2. This vector was designed to change the immune tumor microenvironment. In this study we investigated the immune stimulating effect of Im02 on human primary urothelial cancer specimens or normal urothelium by RNASeq expression analysis. The tissues were transduced with Im02 or an adenoviral vector without expression cassette and were further cultivated for six days. Samples without transduction and cultivation were analysed to determine the status of the microenvironment.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Aljoscha Leusmann

PROVIDER: E-MTAB-7659 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression analysis of human ex vivo cultivated urothelial carcinoma samples transduced with a trivalent adenoviral vector (Im02) for activation of the immune tumor microenvironment.

Project description:The trivalent adenoviral vector Im02 encodes the cDNAs for human 4-1BBL, IL-12 and IL-2. This vector was designed to change the immune tumor microenvironment. In this study we investigated the immune stimulating effect of Im02 on human primary urothelial cancer specimens or normal urothelium by microarray RNA expression analysis. The tissues were transduced with Im02 or an adenoviral vector without expression cassette and were further cultivated for six days. Samples without transduction and cultivation were analysed to determine the status of the microenvironment.

2021-01-01 | E-MTAB-7623 | biostudies-arrayexpress

Single cell RNA-sequencing experiment of human embryonic stem cells (hESCs) upon Wnt stimulation treatment at three time points (4 hours, 24 hours and 3 days)

Project description:Wnt/b-catenin signalling is an evolutionarily conserved mechanism for cell-cell communication implicated in both developmental processes and diseases such as cancer. A main part of this signalling pathway is the stabilization and nuclear translocation of b-catenin, driving the transcriptional regulation of target genes. However, while b-catenin target genes traditionally have been through to be collectively regulated upon Wnt pathway stimulation, this appears in contrast with the non-overlapping patterns of Wnt target gene expression in several contexts, including early mammalian embryogenesis. To address the question whether individual cells exhibits diverse responses to Wnt stimulation, we followed Wnt target gene activation in human embryonic stem cells (hESCs) via single cell RNA-sequencing (scRNAseq) after GSK3 inhibition at 4, 24 and 72 hours of stimulation.

2023-02-23 | E-MTAB-12598 | biostudies-arrayexpress

Cardiac miRNA expression changes induced by prediabetes

Project description:The aim of the experiment was the analysis of key molecular changes with an unbiased, transcriptomics-based approach in a prediabetes model. Small RNA sequencing analysis was applied to explore the expression changes resulted high-fat chow (supplemented with 40% lard) diet for 21 weeks and a single low dose of streptozotocin (20 mg/kg) treatment at week 4. Long-Evans rats were used in the present study. Left ventricular samples(n=6) of both prediabetic and control groups were analyzed.

2020-04-24 | E-MTAB-8204 | biostudies-arrayexpress

Strategic destabilization of K-MT attachments in elderly cells delays senescence

Project description:Chromosomal instability (CIN) refers to the rate at which cells are unable to properly segregate whole chromosomes, leading to aneuploidy. Using young to old-aged human dermal fibroblasts, we observed a dysfunction of the mitotic machinery arising with age that mildly perturbs chromosome segregation fidelity and contributes to the generation of fully senescent cells. Here, we found that elderly cells have an increased number of stable kinetochore-microtubule (k-MT) attachments and decreased efficiency in the correction of improper k-MT interactions. Importantly, chromosome mis-segregation rates in old-aged cells decreased upon both genetic and small molecule enhancement of MT-depolymerizing kinesin-13 activity. Notably, restored chromosome segregation accuracy inhibited the phenotypes of cellular senescence.

2020-02-27 | E-MTAB-8634 | biostudies-arrayexpress

Chinese hamster ovary (CHO) cell Surfaceome LC-MSMS and mRNA expression analysis

Project description:The production of biopharmaceuticals relies on robust cell systems that can produce recombinant proteins at high levels, and grow and survive in the stressful bioprocess environment. Chinese hamster ovary cells (CHO) as the main production hosts offer a variety of advantages including robust growth and survival in a bioprocess environment. Cell surface proteins are of special interest for the understanding of how CHO cells react to their environment while maintaining growth and survival phenotypes, since they enable cellular reactions to external stimuli and potentially initiate signaling pathways. To provide deeper insight into functions of this special cell surface sub-proteome, pathway enrichment analysis of the determined CHO surfaceome was conducted. Enrichment of growth/ survival pathways such as the phosphoinositide-3-kinase (PI3K/AKT), Mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK-STAT) and RAP1 pathways was observed, offering novel insights into how cell surface receptors and ligand mediated signaling enable the cells to grow and survive in a bioprocess environment. When supplementing surfaceome data with RNA expression data, several growth/ survival-receptors were shown to be co-expressed with their respective ligands and thus suggesting self-induction mechanisms, while other receptors or ligands were not detectable. As data about the presence of surface receptors and their associated expressed ligands may serve as base for future studies, further pathway characterization will enable the implementation of optimization strategies to further enhance cellular growth and survival behavior.

2022-10-15 | PXD033581 | Pride

RNA-seq of isolated tumor cells from high grade serous ovarian cancer (HGSOC) patients

Project description:Tumor cells were isolated from solid tumors or ascites from HGSOC patients and enriched for EpCAM expression by antibody magnetic beads (affinity)-based methods and large RNAs (> 200 nt) sequenced (50 bp paired ends) after rRNA depletion (RiboZero). Expression differences between patients with miliary and non-miliary peritoneal tumor spreading were used for a search for new targeted therapies and for biological annotion.

2020-01-01 | E-MTAB-7674 | biostudies-arrayexpress

Epigenome-wide DNA methylation profiling in CD4+ and CD8+ T cells from patients with multiple sclerosis and healthy controls followed during (1st, 2nd and 3rd trimester) and after pregnancy

Project description:Patient with multiple sclerosis improves during pregnancy while temporarily worsening post-partum. The reasons behind the disease modulation during pregnancy remain unknown. In this study, we have investigated the effect of pregnancy on circulating CD4+ and CD8+ T cells from patients with multiple sclerosis and healthy controls to gain a deeper understanding why patients with multiple sclerosis improves during pregnancy. We assessed transcriptomics in CD4+ and CD8+ T cells obtained during (1st, 2nd and 3rd trimester) and after pregnancy (6 weeks post-partum), using the RNA-seq.

2023-08-02 | E-MTAB-12260 | biostudies-arrayexpress

CUT&RUN experiment at four time points in HEK293T and hESC cells, assessing the time-resolved response of β-catenin genomic occupancy upon Wnt signaling activation

Project description:Wnt/β-catenin signaling is a highly organized biochemical cascade that triggers a gene expression program in the signal-receiving cell. The Wnt/β-catenin-driven transcriptional response is involved in virtually all cellular processes during development, homeostasis, and its deregulation causes human disease. However, outstanding questions remain unanswered. A first question concerns cell-specificity: how this response is integrated into lineage-specific choices is still unknown. A second question concerns time: it is not known whether β-catenin associates with its targets simultaneously or in a time-dependent fashion. For instance, while TCF/LEF and other components of the Wnt transcriptional complex are constitutively associated with the chromatin, it is β-catenin arrival, upon Wnt induction, that launches target genes transcription. Therefore, discovering the dynamics of the genome-wide β-catenin binding pattern is required to unambiguously define the direct targets of Wnt signaling To address these questions, we realized a time-resolved atlas of β-catenin genome-wide occupancy in two human cell types, human embryonic kidney cells 293T (HEK293T) and human embryonic stem cells (hESCs). To this end, we treated HEK293T and hESCs with the GSK3 inhibitor/Wnt activator CHIR99021 (10 mM) for 3 days, and assessed β-catenin binding via CUT&RUN-LoV-U (Zambanini et al., 2022) 90 minutes, 4 hours, 24 hours and 3 days after the onset of the stimulation. This approach allowed us to establish that β-catenin repositions to different genomic loci along stimulation time, showing that a definition of Wnt target genes must take into account the time-dimension. Moreover, β-catenin physical targets are largely cell-type specific, as only a subset of them is present across the examined contexts.

2022-09-30 | E-MTAB-12077 | biostudies-arrayexpress

Cell-of-origin epigenetic signatures are maintained during colorectal carcinogenesis

Project description:Colorectal adenomas are precursor lesions of colorectal cancers and represent clonal amplifications of single cells from colonic crypts. DNA methylation patterns specify cell-type identity during cellular differentiation and therefore provide novel opportunities for the molecular analysis of tumors. We have now analyzed DNA methylation patterns in colorectal adenomas and identified three biologically defined subclasses that describe different intestinal crypt differentiation stages. Importantly, colorectal carcinomas could be classified into the same methylation subtypes, reflecting their shared cell-types of origin with adenomas. Further data analysis also revealed significantly reduced overall survival for one of the subtypes. Our results establish a novel concept for understanding the methylation patterns observed in colorectal cancer and provide opportunities for tumor subclassification and patient stratification.

2018-06-12 | E-MTAB-6450 | biostudies-arrayexpress

A phase II trial of weekly nab-paclitaxel for progressive and symptomatic desmoid tumors

Project description:The uploaded datasets contains raw data from our research: columns represent patients, rows represent meta data (patients response, type of sarcoma, etc ...) + the raw gene counts.

2022-09-01 | E-MTAB-12163 | 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