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| Status |
Public on Jun 11, 2021 |
| Title |
FSL-R8-5963_rep1_planktonic |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Listeria monocytogenes |
| Characteristics |
sample type: Planktonic
Stage: Early stationary phase
medium: BHI
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| Treatment protocol |
Early stationary phase cells (8ml; OD600=0.7-0.8) were incubated statically with sterile coupons (n= 20 coupons/isolate) in a sterile petri dish with BHI (20°C for 2 hours) (Chavant and others 2002). Coupons were rinsed three times in PBS to remove non-adherent cells, placed in a new sterile petri dish containing 8 ml BHI broth, and incubated for three days; BHI was replaced daily. For planktonic controls, overnight cultures were diluted with BHI to OD600 0.7-0.8 (total volume: 8 ml) (Chavant and others 2002), and then incubated in test tubes at 20oC, 200 rpm for 24 hours.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Following incubation, coupons were washed three times with sterile PBS to remove non-adherent cells, then immediately mixed with 1:10 volume ice-cold 10% acidified phenol:chloroform (Life Technologies, Grand Island, NY) in ethanol. Biofilm cells were detached from the coupons in stop solution using a spatula and subsequent vortexing. Cells were pelleted (15,300 x g, 20 min, 4°C), coupons removed, and pellets re-suspended in 1 mL TRIzol® (Life Technologies). RNA extraction proceeded as previously described in biological triplicate (Pleitner and others 2014; Raengpradub and others 2008). Sample quality was assessed via the 2100 Bioanalyzer system (Agilent, Foster City, CA). DNA removal was evaluated via qRT-PCR as previously described (Pleitner and others 2014)
RNA libraries were prepared using the Epicentre ScriptSeqTM complete kit (Illumina) and ScriptSeqTM Index PCR primers (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Transient isolate from retail deli
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| Data processing |
Criteria for removal of bases/reads were: Phred33 score <30 or read length <50 bases
Trimmed reads were mapped to L. monocytogenes 10403S using Bowtie2 (v. 2.2.8) (Sciences 2016)
HTSeq (v. 0.6.1) (Lemon and others 2010) determined read counts
DESeq2 (v. 2.1.2) (Love and others 2014) was used to determine significant differences between biofilm and planktonic samples for each isolate
Supplementary_files_format_and_content: HTSeq files for each sample containg gene counts after mapping to 10403S
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| Submission date |
Jun 10, 2021 |
| Last update date |
Jun 11, 2021 |
| Contact name |
Andrea Etter |
| E-mail(s) |
andrea.etter@uvm.edu
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| Organization name |
University of Vermont
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| Department |
Nutrition and Food Science
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| Lab |
Food Microbiology Lab
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| Street address |
109 Carrigan Drive
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| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
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| Platform ID |
GPL21330 |
| Series (1) |
| GSE176617 |
Transcriptomic analysis of biofilm formation in persistent and transient Listeria monocytogenes from the retail deli environment |
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| Relations |
| BioSample |
SAMN19659098 |
| SRA |
SRX11116468 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5369655_Planktonic5963_E1_bowtie.counts.txt.gz |
9.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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