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MetabolomicsAn overlooked prebiotic: beneficial effect of dietary nucleotide supplementation on gut microbiota and metabolites in senescence-accelerated mouse prone-8 mice
Nucleotides (NTs) are regulatory factors in many biological processes and play important roles in the growth, development, and metabolism of living organisms. We used senescence-accelerated mouse prone-8 (SAMP8) to investigate the effects of NTs on the gut microbiota and metabolites. And the promoti...
2022-03-21 | MTBLS4012 | MetaboLights
TranscriptomicsTranscriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection.
Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic...
ORGANISM(S): Eucalyptus camaldulensis 
2012-07-17 | E-GEOD-39369 | biostudies-arrayexpress
TranscriptomicsIndividual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells
Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining da...
ORGANISM(S): Homo sapiens 
2014-02-13 | E-GEOD-37560 | biostudies-arrayexpress
MetabolomicsPreliminary exploration of the ability of HUC-MSCs to restore the lung microbiota and related metabolite disorders in IPF treatment: Combining 16S sequencing and metabolite analysis

Abstract

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive pulmonary disease, and effective therapies to reverse the natural course of IPF are lacking. A growing number of studies have shown that the use of human umbilical cord-derived mesenchymal stem cells (HUC-...

2025-09-01 | MTBLS12922 | MetaboLights
TranscriptomicsNucleotide composition-linked divergence of vertebrate core promoter architecture
Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. ...
ORGANISM(S): Xenopus (Silurana) tropicalis 
2010-12-30 | E-GEOD-21482 | biostudies-arrayexpress
ProteomicsNucleotide pyrophosphatase/phosphodiesterase from Euphorbia characias latex
The low-resolution structure of a nucleotide pyrophosphatase/phosphodiesterase from Euphorbia characias latex (ELNPP) has been determined in solution by means of Small Angle X-ray Scattering (SAXS). To improve the structural resolution of ELNPP a partial sequencing after proteolytic cleavage of the ...
ORGANISM(S): Euphorbia characias 
2022-03-02 | PXD009976 | Pride
Nucleotide pyrophosphatase/phosphodiesterase Euphorbia characias Msms sequencing 
TranscriptomicsDetection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
Whole genome re-sequencing is still a costly method to detect genetic mutations that lead to altered forms of proteins and may be associated with disease development. Since the majority of disease-related single nucleotide variations (SNVs) are found in protein-coding regions, we propose to identify...
ORGANISM(S): Homo sapiens 
2009-06-15 | E-GEOD-16190 | biostudies-arrayexpress
GenomicsDouble fragmentation ChIP-seq provides single nucleotide resolution Tcf4 binding characteristics
ChIP-seq has become the method of choice for studying functional DNA-protein interactions on a genome wide scale. The method is based on co-immunoprecipitation of DNA binding proteins with formaldehyde cross-linked DNA, followed by deep sequencing of immunoprecipitated chromatin fragments, allowing ...
ORGANISM(S): Homo sapiens 
2010-11-01 | E-GEOD-18481 | biostudies-arrayexpress
TranscriptomicsRNA-seq reveals differential gene expression in Staphylococcus aureus at single-nucleotide resolution
Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen. S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (Methicillin-resistant S. aureus) strains. Here we present a method to study differential...
ORGANISM(S): Staphylococcus aureus 
2013-11-07 | E-GEOD-48896 | biostudies-arrayexpress
TranscriptomicsSnapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution
Ribosome assembly in eukaryotes involves the activity of hundreds of assembly factors that direct the hierarchical assembly of ribosomal proteins and numerous ribosomal RNA folding steps. However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking. T...
ORGANISM(S): Saccharomyces cerevisiae 
2014-11-14 | E-GEOD-52878 | biostudies-arrayexpress
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