Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Influence of NSD3 and ESR1 knockdown on gene expression in SUM-44 cells

ABSTRACT: Total RNA was isolated from SUM-44 cells subjected to 5 days of puromycin selection following infection with lentiviral shRNA constructs against NSD3-S or ESR1 as well as LacZ control. Samples were harvested in triplicate and prepared and sequenced simultaneously.

ORGANISM(S): Homo sapiens

SUBMITTER: Gary Hardiman

PROVIDER: E-MTAB-5823 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Characterising the cellular activity of new Fibroblast Growth Factor Receptor tyrosine kinase inhibitors and identification of a gatekeeper mutation in FGFR3 as a mechanism of acquired resistance.

Project description:Fibroblast growth factor receptors (FGFRs) can act as driving oncoproteins in certain cancers due to mutation, over-expression or activating gene fusions and are therefore attractive drug targets. Here we have characterized tumour cell responses to three new inhibitors of FGFR1-3, AZ12576089, AZ12908010 and the clinical candidate AZD4547, making comparisons with the well-characterized FGFR inhibitor PD173074. Using a panel of 16 human tumour cell lines we show that the anti-proliferative activity of AZ12908010 and AZD4547 is strongly linked to the presence of de-regulated FGFR signalling. In contrast, AZ12576089 was also able to inhibit proliferation of cells lacking de-regulated FGFR, suggesting off-target effects. Acquired resistance to targeted tyrosine kinase inhibitors (TKIs) is a growing problem in the clinic. To assess how FGFR-dependent tumour cells may adapt to long-term exposure to FGFR inhibitors we generated a derivative of the KMS-11 myeloma cell line (FGFRY373C) with acquired resistance to AZ12908010 (KMS-11R cells). Basal P-FGFR3, P-FRS2 and P-ERK1/2 and D-type cyclins were all inhibited by AZ12908010 in parental KMS-11 cells whereas these markers were constitutively elevated and refractory to drug in KMS-11R cells. Sequencing of FGFR3 in KMS-11R cells revealed the presence of a heterozygous mutation at the gatekeeper residue, encoding FGFR3V555M. Consistent with this KMS-11R cells were cross-resistant to AZD4547 and PD173074 but remained fully sensitive to AZ12576089, confirming that the anti-proliferative effects of AZ12576089 are not related to FGFR inhibition. These results define the selectivity and efficacy of two new FGFR inhibitors and identify a secondary gatekeeper mutation as a mechanism of acquired resistance to FGFR inhibitors that should be anticipated as clinical evaluation proceeds.

2012-10-02 | E-TABM-1222 | biostudies-arrayexpress

Transcription profiling of human 239T cells shows SUMOylation of DRIL1 directs its transcriptional activity towards leukocyte lineage-specific genes

Project description:SUMOylation of DRIL1 directs its transcriptional activity towards leukocyte lineage-specific genes

2009-06-26 | E-TABM-681 | biostudies-arrayexpress

Transcription profiling of human fibroblast cells from punch skin biopsies obtained from 2 MACS syndrome patients and 4 ethnically matched healthy controls.

Project description:We found a candidate region (with 55 known or predicted genes) that was found to linkage to the MACS syndrome. Because it is transmitted in an autosomal recessive fashion, and given the fact most recessive disorders are caused by loss-of-function mutations often resulting in decreased mRNA levels, we hypothesized that screening the expression of the various genes located within the disease interval may point to candidate genes of interest. We therefore established fibroblast cell lines from punch skin biopsies obtained from 2 patients and 4 ethnically matched healthy controls. We then compared global gene expression using microarrays in the 6 cell lines (all genes contained within the disease interval were represented on the array).

2009-08-01 | E-TABM-735 | biostudies-arrayexpress

Transcription profiling of various cell types isolated from pancreatic islet grafts in Id1/Id3 deficient and wild type mice

Project description:To gain insights into the genetic program activated within the distinct vascular and inflammatory transplant microenvironments in Id1/Id3 deficient and WT mice, we performed a series of gene screening experiments using RNA from total graft tissue as well as from myeloid and endothelial (i.e., CD31+ and ISB4+) cells isolated from the grafts at 1 week post-transplantation.

2008-06-13 | E-TABM-355 | biostudies-arrayexpress

Transcription profiling by array of human untreated endometrial cancer cell lines

Project description:Gene expression array analysis of 8 untreated endometrial cancer cell lines using Illumina human WG6 version 2

2010-09-25 | E-TABM-992 | biostudies-arrayexpress

Transcription profiling of 12 human ovarian clear cell carcinoma cell lines

Project description:12 ovarian clear cell carcinoma cell lines were transcriptomically profiles using the illumina human v6 chip

2008-11-13 | E-TABM-540 | biostudies-arrayexpress

Transcription profiling of mouse B lymphocytes after thapsigargin-stimulated ER stress for 8 and 24 hours to elucidate factors that influence T cell priming

Project description:Time course data from thapsigargin-stimulated ER stress for 8 and 24 hours, in order to elucidate factors that influence T cell priming.

2008-04-16 | E-TABM-240 | biostudies-arrayexpress

Transcription profiling of human KNS42 cells treated with the dual pI3-kinas/mTOR inhibitor PI-103

Project description:Sensitivity to temozolomide (TMZ) is restricted to a subset of glioblastoma patients, with the major determinant of resistance a lack of promoter methylation of the gene encoding the DNA methyltransferase MGMT, although other mechanisms are thought to be active. In a genome-wide screen of paediatric and adult glioma cells, we identified a co-ordinated upregulation of HOX gene expression in the MGMT-independent cell line KNS42. As a recent study has proposed a mechanism for this observation whereby transcriptional activation of the HOXA cluster is reversible by a PI3-kinase inhibitor through an epigenetic mechanism involving histone H3K27 trimethylation, we sought to investigate whether this was active in our system. We thus treated KNS42 cells for 24 hours with the dual PI3-kinase / mTOR inhibitor PI-103 at 5x IC50 and carried out gene expression profiling using Illumina HT-12 microarrays.

2011-01-08 | E-TABM-890 | biostudies-arrayexpress

Thioredoxin-1 Alters Anti-Tumor T Cell Immuno-Metabolic Phenotype

Project description:ABSTRACT Adoptive transfer of tumor epitope reactive T cells is a promising strategy to control tumor growth. However, chronically stimulated T cells expanded for adoptive cell transfer (ACT) are susceptible to cells death in an oxidative tumor microenvironment. Since oxidation of cell surface thiols (c-SH) also alters functionality of proteins, we hypothesized that increased level of thioredoxin, an anti-oxidant molecule that facilitates reduction of proteins by cysteine thioldisulfide exchange, in T cells will result in sustained anti-tumor function. Using Pmel-Trx1 transgenic mouse derived splenic T cells we observed higher c-SH expression that inversely correlated with ROS, and susceptibility to TCR restimulation or oxidation mediated cell death. These Trx1 overexpressing T cells showed CD62Lhi central memory-like (Tcm) phenotype with reduced glucose uptake (2-NBDGlo) and effector function (IFNγlo). Further, using tumor reactive T cells cultured in presence of recombinant Trx resulted in increased dependence of T cells on mitochondrial metabolism and led to improved tumor control. Thus, strategies to increase antioxidant capacity of anti-tumor T cells modulate its immune-metabolic phenotype leading to improved immunotherapeutic control of established tumors.

2021-12-20 | E-MTAB-7571 | biostudies-arrayexpress

Role of CCR2+ myeloid cells in pancreatic Î² cell growth and regeneration

Project description:Pancreas and spleen were microdissected from wild type (C57B6/SV129 background) E14.5 embryos and P0 newborn pups. Pools of 30-60 tissues were used. Tissues were digested for 1 hour at 37Â°C in HBSS/0.1% collagenase A/20 Âµg/ml DNase I, followed by dissociation of the cell clusters into single cells using a non-enzymatic dissociation medium (Sigma). Single cell suspensions were blocked with mouse IgGs and anti-CD16/32 Abs and immunostained with biotin-anti-CD11b (Biolegend) and RPE-conjugated goat anti-CCR2 (R&D Systems), followed by Cy5.5 conjugated streptavidin. CD11b+CCR2+ cell were then isolated by FACS sorting. mRNA from purified cells was prepared using the RNAeasy kit (Qiagen) and run on a MouseWG-6 v2.0 Expression BeadChip.

2017-12-06 | E-MTAB-5427 | biostudies-arrayexpress

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