Ontology highlight
ABSTRACT:
PROVIDER: PRJNA772158 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16388587.fastq.gz | Fastqsanger.gz | |||
| SRR16388587_1.fastq.gz | Fastqsanger.gz | |||
| SRR16388587_2.fastq.gz | Fastqsanger.gz | |||
| SRR16388588.fastq.gz | Fastqsanger.gz | |||
| SRR16388588_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments.
2012-12-01 | GSE32312 | GEO
Project description:Reliably generating rice varieties with low glycemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non‑starch polysaccharide pathway in lowering GI.
2019-02-01 | GSE123616 | GEO
Project description:Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments. Distal colon tissues from Sprague Dawley rats fed a variety of diets (see summary) were removed from RNAlater stabilisation reagent (Sigma, Australia) they had been stored in,, placed in 1 ml of TRIzol® Reagent (Invitrogen, Australia) and homogenised usingbeads (mix of 2.5 mm glass and 0.1 - 1.0 mm diameter silicon-zirconian beads) in a MiniBeadbeater-8 (BioSpec Products Inc., USA). Total RNA was extracted (using TRIzol® Reagent manufacturer's instructions) and further purified using RNAeasy mini spin columns (QIAGEN, Australia) with a DNase on-column digestion as per manufacturer's instructions.RNA integrity was checked using a Bioanalyzer 2100 (Agilent Technologies, USA) andquantified using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). RNA samples with insufficinet quality and quantity were not assayed. The numbers of rats arrayed from each diet were as follows: CON, 5;LAMS, 7; HAMS, 8; HAMSB, 9; LAW, 6; HAW , 8. This gives a total of 43 arrays.
2012-12-01 | E-GEOD-32312 | biostudies-arrayexpress
Project description:A deeper understanding of the genetics of rice grain starch structure is crucial in tailoring grain digestibility and ensuring cooking quality to meet consumer preferences. Significant association peaks on chromosomes 6 and 7 were identified through genome-wide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known and novel genes with high correlation to the proportion of amylose and amylopectin. A novel SNP in the promoter region of Granule Bound Starch Synthase I (GBSS I) was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A novel GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a non-synonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose novel target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related non-communicable diseases.
2016-11-29 | GSE90576 | 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).
| 2533916 | ecrin-mdr-crc
Project description:Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. Japan, especially western and central parts, has seen record high temperatures in the last decade, and the rice kernel quality has decreased; specifically a reduction the first-grade of rice has been seen. In this study, we specifically looked at the harvested rice in a town of the central Kanto-plains (Japan) during the year 2010, which saw day-time temperatures go above the critical limits ranging from 34 to 38C at the final stages of seed development and maturity to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial) were obtained Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki prefecture in September 2010, as grade 1 (labeled as Y1), grade 2 (labeled as Y2), and grade 3 (out-of-grade, labeled as Y3). The research objective was to examine in particular alterations in gene expressions genome-wide in grade 2 (Y2) and grade 3 (Y3) seeds over the grade 1 (Y1) following the high-temperature spike using a high-throughput omic-approach DNA microarray (Agilent 4 x 44K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. Rice seed quality analysis revealed, as expected, low quality in Y3 > Y2 over Y1, in taste, amylose, protein and fatty acid degree, but not in water content. Transcriptome profiling data revealed 124 and 373 up-regulated and 106 and 129 down-regulated genes in Y2 and Y3, respectively. Bioinformatics analysis of differentially expressed genes revealed changes in function of genes related to metabolism, including starch metabolism (e.g., alpha amylase), defense/stress response, fatty acid biosynthesis and hormones. This research provides for the first time the seed transcriptome profile for the classified low grades (2 and out-of-grade) of rice under an actual stressed environmental condition of high temperature.
2016-03-21 | GSE79405 | GEO
Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.
2013-08-06 | GSE49561 | GEO
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants. Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)
2015-12-31 | E-GEOD-60288 | biostudies-arrayexpress
Project description:Ahmad2017 - Genome-scale metabolic model
(iGT736) of Geobacillus thermoglucosidasius (C56-YS93)
This model is described in the article:
A Genome Scale Model of
Geobacillus thermoglucosidasius (C56-YS93) reveals its
biotechnological potential on rice straw hydrolysate
Ahmad Ahmada, Hassan B. Hartmanb, S.
Krishnakumara, David A. Fellb, Mark G. Poolmanb, Shireesh
Srivastavaa
Journal of Biotechnology
Abstract:
Rice straw is a major crop residue which is burnt in many
countries, creating significant air pollution. Thus,
alternative routes for disposal of rice straw are needed.
Biotechnological treatment of rice straw hydrolysate has
potential to convert this agriculture waste into valuable
biofuel(s) and platform chemicals. Geobacillus
thermoglucosidasius is a thermophile with properties specially
suited for use as a biocatalyst in lignocellulosic
bioprocesses, such as high optimal temperature and tolerance to
high levels of ethanol. However, the capabilities of
Geobacillus thermoglucosidasius to utilize sugars in rice straw
hydrolysate for making bioethanol and other platform chemicals
have not been fully explored. In this work, we have created a
genome scale metabolic model (denoted iGT736) of the organism
containing 736 gene products, 1159 reactions and 1163
metabolites. The model was validated both by purely theoretical
approaches and by comparing the behaviour of the model to
previously published experimental results. The model was then
used to determine the yields of a variety of platform chemicals
from glucose and xylose — two primary sugars in rice
straw hydrolysate. A comparison with results from a model of
Escherichia coli shows that Geobacillus thermoglucosidasius is
capable of producing a wider range of products, and that for
the products also produced by Escherichia coli, the yields are
comparable. We also discuss strategies to utilise arabinose, a
minor component of rice straw hydrolysate, and propose
additional reactions to lead to the synthesis of xylitol, not
currently produced by Geobacillus thermoglucosidasius. Our
results provide additional motivation for the current
exploration of the industrial potential of Geobacillus
thermoglucosidasius and we make our model publicly available to
aid the development of metabolic engineering strategies for
this organism.
This model is hosted on
BioModels Database
and identified by:
MODEL1703060000.
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2017-04-12 | MODEL1703060000 | BioModels