Scartelaos histophorus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839847 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
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Project description:Vongsangnak2008 - Genome-scale metabolic
network of Aspergillus oryzae (iWV1314)
This model is described in the article:
Improved annotation through
genome-scale metabolic modeling of Aspergillus oryzae.
Vongsangnak W, Olsen P, Hansen K,
Krogsgaard S, Nielsen J.
BMC Genomics 2008; 9: 245
Abstract:
BACKGROUND: Since ancient times the filamentous fungus
Aspergillus oryzae has been used in the fermentation industry
for the production of fermented sauces and the production of
industrial enzymes. Recently, the genome sequence of A. oryzae
with 12,074 annotated genes was released but the number of
hypothetical proteins accounted for more than 50% of the
annotated genes. Considering the industrial importance of this
fungus, it is therefore valuable to improve the annotation and
further integrate genomic information with biochemical and
physiological information available for this microorganism and
other related fungi. Here we proposed the gene prediction by
construction of an A. oryzae Expressed Sequence Tag (EST)
library, sequencing and assembly. We enhanced the function
assignment by our developed annotation strategy. The resulting
better annotation was used to reconstruct the metabolic network
leading to a genome scale metabolic model of A. oryzae.
RESULTS: Our assembled EST sequences we identified 1,046 newly
predicted genes in the A. oryzae genome. Furthermore, it was
possible to assign putative protein functions to 398 of the
newly predicted genes. Noteworthy, our annotation strategy
resulted in assignment of new putative functions to 1,469
hypothetical proteins already present in the A. oryzae genome
database. Using the substantially improved annotated genome we
reconstructed the metabolic network of A. oryzae. This network
contains 729 enzymes, 1,314 enzyme-encoding genes, 1,073
metabolites and 1,846 (1,053 unique) biochemical reactions. The
metabolic reactions are compartmentalized into the cytosol, the
mitochondria, the peroxisome and the extracellular space.
Transport steps between the compartments and the extracellular
space represent 281 reactions, of which 161 are unique. The
metabolic model was validated and shown to correctly describe
the phenotypic behavior of A. oryzae grown on different carbon
sources. CONCLUSION: A much enhanced annotation of the A.
oryzae genome was performed and a genome-scale metabolic model
of A. oryzae was reconstructed. The model accurately predicted
the growth and biomass yield on different carbon sources. The
model serves as an important resource for gaining further
insight into our understanding of A. oryzae physiology.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180056.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180056 | BioModels
Project description:We compiled the transcriptome by extracting mRNA, reverse transcription and Illumina sequencing, followed by assembly and annotation by comparison with public databases (including; Nr, SwissProt and COG). Quantitative data on the transcription abundance of each putative protein sequence is provided as assesed by the SOAPdenovo_trans assembly tool.
2013-10-28 | E-MTAB-1859 | biostudies-arrayexpress
Project description:This dataset includes RNAseq data of 7 tissues/developmental stages of Lathyrus sativus genotype LSWT11 and 2 tissues with drought- and well-watered treatments of Lathyrus sativus genotypes LS007 and Mahateora. These data were used in the functional annotation pipeline of the Rbp1.0 genome assembly of LS007. The multi-tissue transcriptome was also used to support gene candidate identification by mRNA abundance. Also included is Hi-C sequencing data used to scaffold the assembly into pseudochromosomes
2023-01-31 | GSE223956 | GEO
Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
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Project description:Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins.
2020-07-10 | PXD016962 | Pride
Project description:Here we performed a comprehensive genomic and proteomics analysis of P. stutzeri in aerobic and oxygen-limiting conditions. We combined de novo genome assembly relying on 3rd generation long read sequencing technologies to report the first complete P. stutzeri ATCC14405 genome, which added over 110 kb of sequence and contains 126 full length CDS that were only partially covered in the fragmented short read-based genome assembly available for this strain. With this optimal basis for downstream functional genomics, we next carried out state of the art bottom-up and top-down proteomics analyses to report the most detailed study of proteome remodeling in response to oxygen limitation in P. stutzeri. We identified more than 2900 proteins, i.e. greater than 70% of the theoretical proteome, including 160 annotated small proteins. The proteins included well-established enzymes involved in denitrification and metabolic adaptation to oxygen-limiting conditions, as well as uncharacterized proteins. Notably, we identified 16 novel small proteins that had so far been missed in the genome annotation.
2023-08-04 | PXD037914 | Pride
Project description:With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation, which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the early ZGA-stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes.
2018-05-24 | GSE101843 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
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Project description:We used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation,
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