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SRX20989701: GSM7595606: S.variabile, glucose, R3; Subdoligranulum variabile; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 22.3M spots, 1.7G bases, 656.3Mb downloads

External Id: GSM7595606_r1
Submitted by: INRAE
Study: Effect of supplementation of a minimal culture medium with inulin, corn fiber and pectin, compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota
show Abstracthide Abstract
The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. In Firmicutes species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries. Overall design: To investigate this differential expression, bacterial RNA was extracted after 12h of culture in minimum medium supplemented with one complex carbohydrate or glucose. RNA was extracted using RNAeasy Qiagen kit.
Sample: S.variabile, glucose, R3
SAMN36411081 • SRS18264368 • All experiments • All runs
Library:
Name: GSM7595606
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: RNA was harvested using RNeasy kit (Qiagen) Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer's instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit. Libraries were pooled in equimolar proportions and sequenced on a single read 75pb run, on an Illumina NextSeq500 instrument.
Runs: 1 run, 22.3M spots, 1.7G bases, 656.3Mb
Run# of Spots# of BasesSizePublished
SRR2524339822,274,0381.7G656.3Mb2023-12-01

ID:
28423533

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