GSM4041106: ABTGC rep6; Pseudomonas aeruginosa; RNA-Seq - SRA

SRX6747260: GSM4041106: ABTGC rep6; Pseudomonas aeruginosa; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 16.5M spots, 658.2M bases, 371.6Mb downloads

Submitted by: NCBI (GEO)

Study: Transcriptomic profiles of Pseudomonas aeruginosa PAO1 grown in the presence or absence of mucins or mucin-glycans

PRJNA561292 • SRP218964 • All experiments • All runs

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We use high-throughput sequencing to profile the response of the opportunistic mucosal pathogen Pseudomonas aeruginosa to mucins and mucin-glycans from the mucosal niche. We find that P. aeruginosa undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans. Specifically, nearly all virulence pathways are downregulated in response to these host-produced factors. This study provides a framework for understanding how the host environment regulates bacterial function. Overall design: Examination of differential gene expression in Pseudomonas aeruginosa in response to mucin and mucin sugars

Sample: ABTGC rep6

SAMN12613378 • SRS5297512 • All experiments • All runs

Organism: Pseudomonas aeruginosa PAO1

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: Total RNA was extracted using the MasterPure RNA Purification kit (Lucigen) and residual DNA was removed using the Turbo DNA-free kit (Ambion). The integrity of the total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). 16S, 23S, and 5S rRNA were removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre). Gene expression analysis was conducted via Illumina RNA sequencing (RNA-seq). Libraries were produced using the KAPA RNA HyperPrep kit (Kapa Biosystems). Libraries were sequenced using the Illumina HiSeq platform with a single-end protocol and read lengths of 40 nt or 52 nt.

Experiment attributes:

GEO Accession: GSM4041106

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 16.5M spots, 658.2M bases, 371.6Mb

Run	# of Spots	# of Bases	Size	Published
SRR10008986	16,455,167	658.2M	371.6Mb	2019-10-21

ID:: 8888191

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