Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human cell line and subcutaneous tumor

ABSTRACT: To find different gene expression signature in OVCAR5 cells with PTPRR -WT expression or PTPRR-DA expression compared with control cells, we did RNA-seq analyses.To find different gene expression signature in xenagraft tumors generated from OVCAR5 cells with PTPRR -WT expression or PTPRR-DA expression compared with control cells, we did RNA-seq analyses.

ORGANISM(S): Homo sapiens

PROVIDER: GSE135220 | GEO | 2019/10/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

PTPRR interactome detection using PUP-IT (pupylation-based interaction tagging) Mass Spectrometry

Project description:To further stably express PTPRR (WT)-PafA or PTPRR (DA)-PafA in iPUP OVCAR5 cell, we subcloned PTPRR-WT or DA, respectively, into the PafA-IRES-EGFP plasmid. Each plasmid was packed into a lentivirus and then transduced into iPUP OVACR5 cells for 48 h. GFP-positive cells were sorted by flow cytometry. The expression of PTPRR (WT)-PafA and PTPRR (DA)-PafA was confirmed by western blotting analysis. PTPRR (WT)-PafA or PTPRR (DA)-PafA expressed iPUP OVCAR5 cells were grown to a cell density of about 75% on 10 cm dishes. We followed the protocol established previous. To prepare PUP-IT samples for mass spectrometry analysis, including doxycycline induction, biotin labeling, cell lysis, streptavidin magnetic beads pull-down, trypsin digestion, and peptide cleaning.

2019-10-30 | PXD015352 | Pride

Repurposing of a known antipsychotic drug to target arthritogenic synovial fibroblasts

Project description:We applied quantitative mass spectrometry (MS)-based proteomics to investigate the phosphoproteome of hTNF-stimulated and Amisulpride-treated synovial fibroblasts (SFs), as part of a study aiming to find new potent orally-administered therapeutics to reverse the pathogenic expression signature of arthritogenic SFs. Phosphoproteomics analysis were done by DIA-based phosphoproteomic profiling of synovial fibroblasts. Samples consisted of hTNF-induced WT SFs. Three different time points (5’, 15’, 30’) of hTNF induction were used and compared to cells pretreated with Amisulpride for 1h before being stimulated at similar time points with hTNF (5’, 15’, 30’).

2023-04-11 | PXD035230 | Pride

UPR induction in samples derived from OVCAR5 cancer cells treated with spirocyclic dimer SpiD7

Project description:The objective of this study was to evaluate the transcriptional changes in OVCAR5 cells upon treatment with a spirocyclic α-methylene-γ-butyrolactone dimer SpiD7. To assess if SpiD7 activates Unfolded Protein Response, OVCAR5 cells were treated with SpiD7 for different time points. A time dependent increase in the expression of genes in the hallmark UPR gene set was observed demonstrating induction of UPR.

2021-12-10 | GSE190368 | GEO

Expanding Hematopoietic Stem Cell pool through Fine tuning of Tpo receptor with diabodies.

Project description:Class I cytokine receptors such as Thrombopoietin receptor (MPL) are dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Thrombopoietin (TPO) and its receptor (TpoR), to dimerize TpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism. Here we describe a single-cell transcriptome analysis of 659 human Hematopoietic Stem Cells cultured with different DA. We find several difference between differentiation and activation of signaling pathways compared to TPO.

2021-02-01 | GSE115235 | GEO

DACH1 expression in U87 cells

Project description:Loss or reduction in function of tumor suppressor genes contributes to tumorigenesis. We identified a novel homozygous deletion of DACH1 in gliomas. We generated U87TR-Da glioma cell line, where DACH1 expression could be activated by exposure of cells to doxycycline, and examined changing global gene expression by DACH1 expression. Expression of DACH1 in U87TR-Da cells can be induced by exposure of the cells to doxycycline. We analyzed gene expression profiles of DACH1-induced/repressed U87TR-Da cells. And we also compared gene expression profiles of DACH1-induced/repressed U87TR-Da cells under different culture condition, DMEMF(serum-containing) and NBE(serum-free)

2011-07-19 | E-GEOD-19678 | biostudies-arrayexpress

CD4+ cell transcriptional profiling by RNA sequencing

Project description:<p>We use next generation sequencing to investigate the different transcriptomes of closely related CD4+ T-cells from healthy human donors to elucidate the genetic programs that underlie their specialized immune functions. Six cell types were included: Regulatory T-cells (CD25hiCD127low/neg with >95% FOXP3+ purity), regulatory T-cells activated using PMA/ionomycin, CD25-CD45RA+ ('naive' helper T-cells), CD25-CD45RO+ ('memory' helper T-cells), activated Th17 cells (>98% IL17A+ purity) and activated IL17-CD4+ T-cells (called 'ThPI'). Poly-T capture beads were used to isolate mRNA from total RNA, and fragment sizes of ~200 were sequenced from both ends on Illumina's genome analyzer. We confirm many of the canonical signature genes of T-cell populations, but also discover new genes whose expression is limited to specific CD4 T-cell lineages, including long non-coding RNAs. Additionally, we find that genes encoded at loci linked to multiple human autoimmune diseases are enriched for preferential expression upon T-cell activation, suggesting that an aberrant response to T-cell activation is fundamental to pathogenesis.</p>

| phs000626 | dbGaP

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth

Project description:Different fibroblast cells (eight in total) with different inhibitory capacity were analyzed and compared for their gene expression profile by whole genome microarray. Different fibroblast cells (eight in total) were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1) in order to find out gene expression differences.

2014-05-01 | E-GEOD-57199 | biostudies-arrayexpress

Characterization of human iPSC-derived dopaminergic neurons with 16p11.2 CNVs

Project description:We studied human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neuron populations carrying CNVs of 16p11.2 duplication and 16p11.2 deletion. Previously, healthy human iPSCs were edited using CRISPR-Cas9 method to produce isogenic lines with 16p11.2 deletion or 16p11.2 duplication. We differentiated these isogenic iPSC lines into neural precursor cells and dopaminergic neurons and collected RNA samples for gene expression analyses with RNA sequencing. Our aim was to identify differences in the expression of synaptic markers, neuronal differentiation markers, and neuron specific receptors that affect functionality of the neurons with 16p11.2 CNVs compared to isogenic control lines. We also studied physiological properties of these isogenic iPSC-derived DA neurons with 16p11.2 CNVs. In addition, we studied expression and activation of a specific molecular pathway KCTD13-RHOA in the iPSC derived DA neuron populations with 16p11.2 CNVs.

| EGAS00001005137 | EGA

Genome-wide maps of H3K79Me3 binding sites in ovarian cancer cell line OVCAR5 and expression profile of DOT1L knockdown OVCAR5 cells (ChIP-seq)

Project description:This study characterized the genome-wide binding of histone 3 lysine 79 tri-methylation and expression profile of DOT1L knockdown in OVCAR5 cells.

2022-11-08 | GSE199473 | GEO

Genome-wide maps of H3K79Me3 binding sites in ovarian cancer cell line OVCAR5 and expression profile of DOT1L knockdown OVCAR5 cells (RNA-seq)

Project description:This study characterized the genome-wide binding of histone 3 lysine 79 tri-methylation and expression profile of DOT1L knockdown in OVCAR5 cells.

2022-11-08 | GSE199472 | 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