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SRX8177522: GSM4498574: Faecalicatena contorta 588 Galactose 2; Faecalicatena contorta; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 18.4M spots, 936.8M bases, 315.7Mb downloads

Submitted by: NCBI (GEO)
Study: RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides
show Abstracthide Abstract
Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1% of the overall average RPKM expression level. READS WERE ANALYZED .......GABRIEL FILL IN Results: We identified novel polysaccharide utiilization loci in 5 strains of human gut bacteria Overall design: rRNA-depleted, mRNA profiles of human gut bacteria on respective seaweed polysaccharides run on Illumina Hi-Seq platform.
Sample: Faecalicatena contorta 588 Galactose 2
SAMN14732718 • SRS6537219 • All experiments • All runs
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Qiagen Rneasy kit and rRNA depleted with Microbe Express Kit (Thermo Fisher) RNA libraries were prepared for sequencing using standard Illumina protocols
Experiment attributes:
GEO Accession: GSM4498574
Links:
Runs: 1 run, 18.4M spots, 936.8M bases, 315.7Mb
Run# of Spots# of BasesSizePublished
SRR1161125718,369,255936.8M315.7Mb2020-09-01

ID:
10661711

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