Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1111688 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, we used the illumina high throughput sequencing approach (Sequencing-By-Synthesis, or SBS) to develop the sequence resource of black pepper. To identify micro RNAs functioning in stress response of the black pepper plant, small RNA libraries were prepared from the leaf and root of Phytophthora capsici infected plants, leaves from drought stressed and control plants.
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Project description:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.
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Project description:KNU_NPClab-LCMS_2023_47peppers (white peppers, black peppers and a red pepper)
2024-01-14 | MSV000093869 | MassIVE
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress
Project description:In this study, we have evaluated the proteomic changes that occur in Piper nigrum L.(black pepper) after infection by the pathogen Phytophthora capsici. We report novel leaf proteins from black pepper identified by an integrated transcriptome-assisted label-free quantitative proteomics pipeline. Several previously described methods were used to create this data set. Detached leaves were inoculated with either mock treatment, or the oomycete pathogen and small tissue samples only around the site of inoculation were collected for protein sample preparations. In order to quantify protein abundance in the samples being compared, we used a label free method of spiking samples with a known ratio of pre-digested peptide samples to normalize endogenous protein abundance in the MS detection. Our study attempts to explain the basal immune components of black pepper when challenged with P. capsici.
2016-07-07 | PXD003887 | Pride
Project description:The experiments were performed to elucidate the enigmatic enzymatic formation of the pungent principle, piperine, from black pepper (Piper nigrum L.), the world´s most popular spice. Based a differential RNA-Seq approach including immature fruits, flowers, and leaves, the gene encoding piperine synthase, encoding a BAHD-type acyltransferase and several other candidate genes encoding various enzymatic functions in the biosynthetic pathway were identified. Recombinant piperine synthase and additional promiscuous piperamide synthases were used to facilitate the microbial production of a broad range of medicinally relevant piperamides. Subsequent investigations will also include the identification of enzymatic steps in the phenylpropanoid pathway and the amino acid derived biosynthesis of piperidine Based on the assumption that piperine encoding genes are highly expressed shortly before the slope of piperine accumulation reaches its maximum, RNA from greenhouse grown black pepper plants was extracted from young fruits at two different stages of development, flowers, and leaves were harvested for a differential RNA-Seq approach. Candidate transcripts associated with piperine biosynthesis were identified by comparative transcript abundance and sequence annotation tools.
2021-04-28 | E-MTAB-9029 | biostudies-arrayexpress
Project description:KNU_NPClab-LCMS_2023_47peppers (white peppers, black peppers and a red pepper)
2024-01-14 | MSV000093869 | GNPS
Project description:Piperine Biosythesis in Black Pepper
| PRJEB38192 | ENA