Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IKK in mesothelioma

ABSTRACT: perform gene expression silencing for both IKKs in AE17, AB2 and KPM1 cells using lentiviral shRNA pools. After validating gene silencing, RNA was extracted from both parental (shC) and daughter cells (shChuk, shIkbkb) and was send for RNAsequencing in order to define possible target genes, up or down regulated upon gene expression manipulation with lentiviral shRNA. These cell lines (parental and daughter) were evaluated in vitro for the role of IKKs in cell proliferation, survival and clonogenicity and in vivo for their impact in MPM development upon intrapleural injection in mice

ORGANISM(S): Mus musculus

PROVIDER: GSE129984 | GEO | 2025/04/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The effects of silencing PCYOX1 on the proteome of murine fibroblast cells 3t3-L1 differentiated to adipocyte-like cells

Project description:In order to evaluate the impact of PCYOX1 deletion on adipogenesis, we applied a label-free mass spectrometry-based proteomic approach to compare the proteome of 3T3-L1 differentiated for 9 days to adipocytes after PCYOX1 gene silencing. Pcyox1 was silenced using shRNA lentiviral particles. Control cells were treated with shRNA lentiviral particles containing a negative construct.

2023-05-10 | PXD039943 | Pride

GPM6B regulates osteoblast differentiation and induction of mineralization by controlling cytoskeleton and matrix vesicle release.

Project description:Analysis of GPM6B silenced osteogenic hMSC at gene expression level. Analysis is showing significant changes in genes involved in cytoskeleton organization and biogenesis. Immunocytochemistry confirms changed distribution of actin filaments and change in shape and in size of focal adhesions upon GPM6B silencing. Moreover, we demonstrated that production and release of ALP-positive matrix vesicles (MVs) was reduced. In conclusion, we identified GPM6B as a novel regulator of osteoblast differentiation and bone formation and thereby demonstrating the significance of cytoskeleton organization for MV production and eventual mineralization. Total RNA obtained from osteogenic hMSC, 7days after shRNAi lenti viral transductions with 3 different GPM6B silencing constructs (sh1, sh2, sh3) compared to 3 different controls (shC:non-silencing shRNA, tGFP: tGFP control vector and Mock: mock transduced cells)

2011-06-01 | E-GEOD-26004 | biostudies-arrayexpress

shRNA RNA-seq from K562 (ENCSR936VPP)

Project description:RNA-seq on K562 cells treated with a control shRNA against no target. (k562-shC) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-11-08 | GSE88657 | GEO

Transcriptomic analysis by AmpliSeq Ion Torrent to study the involvement of LINC00707 in the regulation of TGFβ target genes in HaCaT cells

Project description:The aim of this work was to elucidate the role of the lncRNA LINC00707 in HaCaT cells and study whether its downregulation mimics the effects of TGFβ treatment. To this end we used the HaCaT cells that were either transfected with a non-targeting shRNA (shC) and treated with TGFβ1 for 24 h (shC+TGFβ) or stably transfected with two different shRNAs targeting LINC00707 (shLINC00707#2 and shLINC00707#3). Then we analysed gene expression using Ion torrent AmpliseqTM.

2023-06-02 | E-MTAB-12980 | biostudies-arrayexpress

A novel therapeutic strategy targeting the mesenchymal phenotype of malignant pleural mesothelioma by suppressing LSD1 [array]

Project description:Transcriptome analysis following knock down of LSD1 in ACC-MESO-1 cells. Malignant pleural mesothelioma (MPM) is a highly aggressive tumor that has a low overall survival; however, no significant treatment advances have been made in the past 15 years. In this study we investigated whether targeting lysine-specific demethylase 1 (LSD1/KDM1), a histone-modifying enzyme responsible for demethylating histone H3 lysine 4 and lysine 9, could represent a novel therapeutic strategy for patients with MPM. We found that suppressing LSD1 induces an epithelial phenotype in sarcomatoid MPM cells, while attenuating the mesenchymal phenotype sensitized MPM cells to cisplatin-induced apoptosis through the FAK pathway. To investigate the potential mechanisms underlying FAK pathway activation, we performed transcriptome analysis using two different shRNA constructs against the LSD1.

2021-08-10 | GSE181735 | GEO

Quantification of histone H3 and H4 modifications by mass spectrometry in wildtype and MCM2-2A mutants of mice ESCs

Project description:During DNA replication modified parental histones H3-H4 are segregated almost symmetrically to the two daughter DNA strands enabling mitotic inheritance of histone PTMs. Whether heritable histone modifications confer epigenetic regulation by maintaining chromatin states and gene expression is unclear. Using MCM2 histone-binding mutant embryonic stem cells (ESCs) and mass spectrometry, we show that asymmetric segregation of parental histones to the leading strand causes imbalanced inheritance of histone H3K27 methylations to daughter cells.

2023-08-30 | PXD020326 | Pride

Transcriptional effects of lentiviral vector-mediated PDK1 gene silencing in ovarian cancer xenografts

Project description:This experiment was designed to investigate the effect of PDK1 silencing on tumor growth, metabolism, and microenvironment modulation in vivo. Tumors were established in NOD/SCID mice by subcutaneous (s.c.) injection of an highly glycolytic ovarian cancer cell line (OVCAR3) transduced with lentiviral vectors encoding PDK1-specific shRNA and selected in puromycin-containing medium. These cells had >70% reduced expression of PDK1 protein in vitro. OVCAR3 cells transduced with a scrambled shRNA lentiviral vector were used as control. Total RNA was extracted from tumor samples and hybridized on Affymetrix GeneChip™ PrimeView™ Human Gene Expression Arrays. Transcriptome analysis was performed with RNA purified from 5 different tumor samples per group (n=5 mice/shRNA and n=5 mice/shPDHK1), obtained from different mice sacrificed at equivalent tumor volumes (200 mm3).

2020-12-31 | E-MTAB-9877 | biostudies-arrayexpress

Expression profiling of Burkitt's lymphoma cells 24h after FOXM1 shRNA or MYB shRNA lentivirus-mediated transduction

2009-07-27 | GSE17172 | GEO

The effect of THADA knockdown on Huh7 cells

Project description:We use lentivirus carrying shRNA for THADA to evaluate the efect of THADA knockdown in Huh7 cells. The pGIPZ shRNA plasmid specific to human THADA (clone ID V3LHS_318037 Open Biosystems, Inc.) or the pGIPZ non-silencing shRNAmir lentiviral plasmid (as a control) was cotransfected with the pPACKH1 plasmid mix in HEK 293 cells. Stable clones of Huh7 cells with THADA knockdown were routinely maintained in a medium containing of puromycin (500ng/ml)

2015-08-01 | E-GEOD-65233 | biostudies-arrayexpress

Expression profiling of Burkitt's lymphoma cells 24h after FOXM1 shRNA or MYB shRNA lentivirus-mediated transduction

Project description:Human Burkitt's lymphoma ST486 cells were transduced with non-target control shRNA lentiviral vectors, FOXM1 shRNA, and MYB shRNA lentiviral vectors. Total RNA was isolated 24h later. cRNA was produced with the standard one-step IVT protocol (Affymetix) and hybridized in U95Av2 gene chips (Affymetrix). Experiment consists in 3 independent samples: Expression profiling of Burkitt's lymphoma cells 24h after non-target control shRNA lentiviral mediated transduction. Expression profiling of Burkitt's lymphoma cells 24h after FOXM1 shRNA lentiviral mediated transduction. Expression profiling of Burkitt's lymphoma cells 24h after MYB shRNA lentiviral mediated transduction. Data processing performed using MAS5 or GCRMA.

2009-07-27 | E-GEOD-17172 | 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