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NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

ABSTRACT: Pancreatic cancer-derived cells NP-18 underwent four rounds of treatment with increasing doses of an adenoviral vector encoding TK enzyme and GCV. Surviving cells were termed NP-18AR and displayed decreased sensitivity to treatment. This experiment analyses the transcriptomic effect of TK/GCV treatment on NP-18AR as compared to that of NP-18 cells. Two-condition experiment, where response to treatment in naïve cells (NP-18) was compared to response to treatment in previously treated resistant cells (NP-18AR). Biological replicates: samples from 3 independently generated and independently treated NP-18AR lines (NP-18AR1, NP-18AR2 and NP-18AR3) were hibridized with 3 independently treated samples of NP-18 cells. A total of 9 hybridizations were performed, 2 for NP-18AR1 (including 1 dye-swap), 4 for NP-18AR2 (including 2 dye swaps) and 3 for NP-18AR3 (including 1 dye-swap).

ORGANISM(S): Homo sapiens

SUBMITTER: Abate-Daga D

PROVIDER: S-ECPF-GEOD-17137 | biostudies-other | 2010 Oct

REPOSITORIES: biostudies-other

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NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

2010-07-16 | GSE17137 | GEO

NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

Project description:Pancreatic cancer-derived cells NP-18 underwent four rounds of treatment with increasing doses of an adenoviral vector encoding TK enzyme and GCV. Surviving cells were termed NP-18AR and displayed decreased sensitivity to treatment. This experiment analyses the transcriptomic effect of TK/GCV treatment on NP-18AR as compared to that of NP-18 cells. Two-condition experiment, where response to treatment in naïve cells (NP-18) was compared to response to treatment in previously treated resistant cells (NP-18AR). Biological replicates: samples from 3 independently generated and independently treated NP-18AR lines (NP-18AR1, NP-18AR2 and NP-18AR3) were hibridized with 3 independently treated samples of NP-18 cells. A total of 9 hybridizations were performed, 2 for NP-18AR1 (including 1 dye-swap), 4 for NP-18AR2 (including 2 dye swaps) and 3 for NP-18AR3 (including 1 dye-swap).

2010-07-16 | E-GEOD-17137 | biostudies-arrayexpress

Robust learning for optimal treatment decision with NP-dimensionality.

Project description:In order to identify important variables that are involved in making optimal treatment decision, Lu, Zhang and Zeng (2013) proposed a penalized least squared regression framework for a fixed number of predictors, which is robust against the misspecification of the conditional mean model. Two problems arise: (i) in a world of explosively big data, effective methods are needed to handle ultra-high dimensional data set, for example, with the dimension of predictors is of the non-polynomial (NP) order of the sample size; (ii) both the propensity score and conditional mean models need to be estimated from data under NP dimensionality. In this paper, we propose a robust procedure for estimating the optimal treatment regime under NP dimensionality. In both steps, penalized regressions are employed with the non-concave penalty function, where the conditional mean model of the response given predictors may be misspecified. The asymptotic properties, such as weak oracle properties, selection consistency and oracle distributions, of the proposed estimators are investigated. In addition, we study the limiting distribution of the estimated value function for the obtained optimal treatment regime. The empirical performance of the proposed estimation method is evaluated by simulations and an application to a depression dataset from the STAR*D study.

| S-EPMC5544015 | biostudies-literature

T1E-18 vs T1E-18 Indole

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 strain grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.

2013-03-15 | E-MEXP-3822 | biostudies-arrayexpress

T1E-18 vs T1E-18 Ampicillin

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 grown in the presence of ampicillin (100 ug/ml) compared with the same cells grown in absence of ampicillin.

2013-03-15 | E-MEXP-3824 | biostudies-arrayexpress

Methylome analysis of 18 wild-type and mutant mouse ES, NP and MEF cells

Project description:The analysis of the 18 methylomes comprise 3 biological replicates of TDG+/- ES cells, 3 biological replicates of TDG-/- ES cells, 3 biological replicates of TDG+/- NP cells, 3 biological replicates of TDG-/- NP cells, 3 biological replicates of TDG+/+ MEF cells and 3 biological replicates of TDG-/- MEF cells.

2011-02-24 | GSE27468 | GEO

Two experts and a newbie: [18F]PARPi vs [18F]FTT vs [18F]FPyPARP-a comparison of PARP imaging agents.

Project description:PurposeImaging of PARP expression has emerged as valuable strategy for prediction of tumor malignancy. While [18F]PARPi and [18F]FTT are already in clinical translation, both suffer from mainly hepatobiliary clearance hampering their use for detection of abdominal lesions, e.g., liver metastases. Our novel radiotracer [18F]FPyPARP aims to bridge this gap with a higher renal clearance and an easily translatable synthesis route for potential clinical application.MethodsWe developed a less lipophilic variant of [18F]PARPi by exchange of the fluorobenzoyl residue with a fluoronicotinoyl group and automated the radiosyntheses of the three radiotracers. We then conducted a comparative side-by-side study of [18F]PARPi, [18F]FPyPARP, and [18F]FTT in NOD.CB17-Prkdcscid/J mice bearing HCC1937 xenografts to assess xenograft uptake and pharmacokinetics focusing on excretion pathways.ResultsTogether with decent uptake of all three radiotracers in the xenografts (tumor-to-blood ratios 3.41 ± 0.83, 3.99 ± 0.99, and 2.46 ± 0.35, respectively, for [18F]PARPi, [18F]FPyPARP, and [18F]FTT), a partial shift from hepatobiliary to renal clearance of [18F]FPyPARP was observed, whereas [18F]PARPi and [18F]FTT show almost exclusive hepatobiliary clearance.ConclusionThese findings imply that [18F]FPyPARP is an alternative to [18F]PARPi and [18F]FTT for PET imaging of PARP enzymes.

| S-EPMC8803746 | biostudies-literature

Metabolomics analysis of liver reveals profile disruption in bovines upon steroid treatment

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2018-05-08 | MTBLS436 | MetaboLights

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2017-11-01 | GSE86503 | GEO

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