Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic profiling of the FaDu cell line and derived subclones using amplicon-based targeted sequencing

ABSTRACT: Mutational profiling by targeted next-generation sequencing of a SCCHN cell line model and single-cell derived subclones displaying varying sensitivity to cisplatin was used to determine the extent of intratumoral heterogeneity and to dissect the molecular mechanisms involved in primary cisplatin resistance and treatment-induced clonal evolution.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Ingeborg Tinhofer

PROVIDER: E-MTAB-6021 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response of Cupriavidus metallidurans CH34 to different Pt-species

Project description:Response of Cupriavidus metallidurans CH34 to cisplatin, Pt(IV)chloride and Au-NP In this study 7 different treatments were performed (first 2 as 3 replicates) to acquire expression profiles of the total genome of Cupriavidus metallidurans

2016-02-27 | E-GEOD-78723 | biostudies-arrayexpress

MiSeq paired-end sequencing of HEK293T cells stably expressing a Cas9/gRNA-dependent editable reporter vector to test novel nucleobase-editing techniques

Project description:The goal of these experiments were to test the on-target and target-adjacent editing efficiencies of different single-nucleobase editing systems. Previous studies have shown that tethering DNA mutating enzymes to Cas9-nickase-UGI complexes results in editing of chromosomal DNA. However, these editing events encompass undesirable target-adjacent nucleobase edits. Here, we characterize a novel approach that reduces the frequency of target-adjacent editing while maintaining a high level of on-target editing.

2020-02-23 | E-MTAB-8742 | biostudies-arrayexpress

Genome-scale CRISPR knockout screen for a Dengue virus mutant

Project description:Unbiased forward genetic screen to identify host factors for a Dengue virus mutant

2023-06-30 | E-MTAB-11119 | biostudies-arrayexpress

Gene expression profiles in isolated proximal tubules and whole kidneys of rats after cisplatin-administration

Project description:To clarify the effects of cisplatin (cis-diamminedichloroplatinum II, CDDP) on the gene expression profiles in renal proximal tubules, microarray analyses were carried out using total RNA samples isolated from microdissected proximal tubules and whole kidneys. The molecular events underlying acute kidney injury (AKI) in the proximal tubules of rats with cisplatin-induced nephrotoxicity were successfully clarified with 17,000 transcripts. Renal proximal tubules were isolated under microscopy, and transcriptome data were collected with Rat Genome Survey MicroarrayÂ® (Applied Biosystems)

2013-12-24 | E-GEOD-37133 | biostudies-arrayexpress

RNA-seq comparing allergen-trained versus untrained human monocyte-derived macrophages after HDM challenge

Project description:Mibrobial Patterns can induce trained innate immunity in macrophages. We tested whether innate memory can be elicited by stimulating macrophages with a house dust mite extract for 24h before washout and a resting phase of 5 days. Subsequently, macrophages were exposed to HDM for 24h and we analyzed the gene expression post-challenge.

2021-12-31 | E-MTAB-9210 | biostudies-arrayexpress

RNA-seq of human monocyte-derived macrophages comparing healthy versus house dust mite-allergic donors

Project description:Human monocyte-derived macrophages (MDM) from HDM-allergic donors were compared to MDM from healthy donors. CD14+ monocytes were isolated from donated blood and differentiated in the presence of GM-CSF and TGFb (alveolar-like MDM) for 7 days before havest of RNA

2021-12-31 | E-MTAB-9215 | biostudies-arrayexpress

RNA-seq comparing allergen-trained versus untrained human monocyte-derived macrophages

Project description:Mibrobial Patterns can induce trained innate immunity in macrophages. We tested whether innate memory can be elicited by stimulating macrophages with a house dust mite extract for 24h before washout, and analyzed the gene expression after 5 days post-exposure.

2021-12-31 | E-MTAB-9214 | biostudies-arrayexpress

Tumor Growth and Prognosis of Squamous Cell Carcinoma of the Head and Neck is Linked to Protein Kinase C Alpha

Project description:Protein Kinase C alpha (PKC) is a critical mediator of cell signaling and cancer growth. We show that PKC inhibitors decrease proliferation in squamous cell carcinoma of the head and neck (SCCHN) cells and abrogate growth of SCCHN tumors in mouse xenografts. Analysis of gene expression arrays reveals that PKC regulates cell cycle genes required for DNA synthesis. In particular, PKC increases cyclin E protein expression, cyclinE/cdk2 complex formation, and transcription of cyclin E and E2F target genes. Consistent with this mechanism, expression of cyclin E rescues the block in DNA synthesis caused by PKC inhibition. In SCCHN tissue, PKC and cyclin E expression increase progressively from normal and dysplastic to malignant human head and neck tissue. Furthermore, PKC expression correlates with poor prognosis in SCCHN. These results demonstrate that PKC regulates growth by stimulating DNA synthesis through cyclin E and E2F and identify PKC as a therapeutic target that is highly expressed in aggressive SCCHN. Keywords: time course; dose response

2009-03-22 | GSE10299 | GEO

Unexpected roles of ATP11B in platinum resistance

Project description:Platinum compounds display clinical activity against a wide variety of solid tumors. However, resistance to these agents is a major limitation in cancer therapy. Reduced platinum uptake and increased platinum export are examples of resistance mechanisms that limit the extent of DNA damage. Here, we report the discovery and characterization of the role of ATP11B, a P-type ATPase membrane protein, in cisplatin resistance. ATP11B gene silencing restored the sensitivity of ovarian cancer cell lines to cisplatin in vitro. Combined therapy of cisplatin and ATP11B-siRNA significantly decreased cancer growth in mice bearing ovarian tumors derived from cisplatin-sensitive and -resistant cells. In vitro mechanistic studies on cellular platinum content and cisplatin efflux-kinetics indicated that ATP11B enhances the export of cisplatin from cells. The co-localization of ATP11B with fluorescent cisplatin and with vesicular trafficking proteins such as syntaxin-6 (STX6) and vesicular associated membrane protein 4 (VAMP4) strongly suggests that ATP11B contributes to secretory vesicular transport of cisplatin from Golgi to plasma membrane. In conclusion, silencing ATP11B expression might be a therapeutic strategy to overcome cisplatin resistance. We performed the transfection of control-siRNA and ATP11B-siRNA to both cisplatin-sensitive A2780-PAR and cisplatin-resistant A2780-CP20 cells respectively.

2013-01-23 | E-GEOD-43694 | biostudies-arrayexpress

Gene expression from head and neck squamous cell carcinoma (SCCHN) cancer cells before and after figitumumab

Project description:Patients with palliative SCCHN were treated with figitumumab, an IGF-1R inhibitor. This receptor plays an important role in cell growth, proliferation and differentiation and is often overexpressed in SCCHN. No significant clinical activity was observed in our study We used microarray to establish hypothesis for treatment resistance

2011-08-10 | GSE31287 | GEO

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