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A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

ABSTRACT: A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

PROVIDER: PRJNA747256 | ENA |

REPOSITORIES: ENA

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A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

Project description:A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

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A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

Project description:We first treated LX-2 cells with vehicle or HHT (1μM and 5μM) for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated LX-2 cells. HHT-induced expression changes were obtained based on the resultant data.

2021-07-18 | GSE180243 | GEO

A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

Project description:We first treated liver cancer cells with vehicle or HHT for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated liver cancer cells. HHT-induced expression changes were obtained based on the resultant data.

2022-01-21 | GSE193897 | GEO

Optimal settings of mass spectrometry open search strategy for higher confidence

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Alterations in soybean gene expression profile after foliar application of lipo-chitooligosaccharide (LCO) from Bradyrhizobium japonicum under sub-optimal temperature

Project description:Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChipÂ® Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data. Soybean seedlings grown at optimal temperature (25 Â°C) were exposed to sub-optimal temperature (15 Â°C). After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Total RNA was extracted and microarray analysis was performed using Affymetrix GeneChipÂ® Soybean Genome Arrays.

2010-03-20 | E-GEOD-20972 | biostudies-arrayexpress

Alterations in soybean gene expression profile after foliar application of lipo-chitooligosaccharide (LCO) from Bradyrhizobium japonicum under sub-optimal temperature

Project description:Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data.

2010-03-20 | GSE20972 | GEO

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Drug repositioning for gynecologic tumors: a new therapeutic strategy for cancer.

Project description: Not available

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Optimal settings of mass spectrometry open search strategy for higher confidence

Project description:More than half of the mass spectra could not be identified in most proteome mass spectrometry experiments. Various modifications have been considered as a major reason. Open search strategy was then introduced to solve this problem, however, lacking thorough quality assessment using independent information. Here, we used the “Suspicious Discovery Rate (SDR)” based on the translatome sequencing (RNC-seq) as an independent source to assess the proteome open search strategy. We found that the open search strategy increased the spectra utilization with the cost of increasing suspicious identifications that lacks translation evidence. We further suggested that restricting the peptide FDR below 0.1% would efficiently control the suspicious identifications of open search methods and enhanced the confidence of the peptide identification with modifications than the narrow window search. These results facilitated the proper use of open search methods for higher quality of proteome identifications with the information of post-translational modifications and single amino acid polymorphisms

2018-10-04 | GSE112623 | GEO

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