NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4041113 Query DataSets for GSM4041113
Status Public on Oct 20, 2019
Title Glycans rep 1
Sample type SRA
 
Source name Planktonic bacterial cultures
Organism Pseudomonas aeruginosa
Characteristics strain: PAO1
growth medium: ABTGC defined medium
growth time: 5 h
Growth protocol Batch cultivation of Pseudomonas aeruginosa was carried out shaking at 37 °C in LB. Overnight cultures were diluted to an OD600 of 0.01 medium with or without (0.5%) MUC5AC, (0.5%) MUC5B, or (0.01%) MUC5AC-glycans and grown for 5 h at 37 °C in a static 96-well microtiter plate.
Extracted molecule total RNA
Extraction 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Planktonic bacterial cultures
Data processing Illumina genome analyzer modules Firecrest and Bustard were used for image analysis and base-calling, respectively.
Sequence reads were mapped onto the P. aeruginosa PAO1 reference genome, which is available for download from the Pseudomonas Genome Database (http://www.pseudomonas.com) using the Burrows Wheeler algorithm on the Galaxy server.
Read counts were quantified in R thes files are provided as processed data)
Gene expression values were normalized based on library size and differentially expressed genes were identified using a negative binomial test with a false discovery rate (FDR) less than 0.05.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: comma-delimited text files with raw read counts
 
Submission date Aug 21, 2019
Last update date Oct 20, 2019
Contact name Katharina Ribbeck
E-mail(s) ribbeck@mit.edu
Organization name Massachusetts Institute of Technology
Department Biological Engineering
Lab Ribbeck
Street address 21 Ames St
City Cambridge
State/province Massachusetts
ZIP/Postal code 02142
Country USA
 
Platform ID GPL18644
Series (1)
GSE136097 Transcriptomic profiles of Pseudomonas aeruginosa PAO1 grown in the presence or absence of mucins or mucin-glycans
Relations
BioSample SAMN12613386
SRA SRX6747267

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap