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Sample GSM4279696 Query DataSets for GSM4279696
Status Public on Jan 21, 2022
Title 1p
Sample type SRA
 
Source name 3OC12-treated
Organism Lactiplantibacillus plantarum
Characteristics strain: WCFS1
Extracted molecule total RNA
Extraction protocol Frozen sample aliquots thawed at room temperature and pelleted to remove residual RNA Later before treating with 400 µL Lysozyme Solution (1 mg mL-1 lysozyme, 40 mM EDTA, pH 8) for 1 h at 37 °C. Lysozyme treated cells were pelleted and resuspended in RNAzol RT following the manufacturer’s protocol for large RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing raw MiSeq reads were trimmed with Trimmomatic 0.33 (HEADCROP:8, LEADING:20, SLIDINGWINDOW:5:20, MINLEN:50)
Trimmed reads were mapped to the closed L. plantarum WCFS1 genome (GenBank accession GCA_000203855.3) with Bowtie 2 (“-very-sensitive” parameter).
Statistically significant differentially expressed genes were determined by analyzing raw read counts with the R package DESeq2 version 1.8.1 (Love et al., 2014). Size factors to normalize for sequencing depth were generated by both R packages DESeq2 and cqn version 1.14 (Hansen et al., 2012).
Comparisons were made between controls and samples treated with 3OC12. A statistical cutoff for differentially expressed genes of adjusted P value (Benjamin and Hockberg adjustment) was set at < 0.05, where genes satisfying this criteria were defined as differentially expressed.
Annotations for these genes were obtained from the NCBI website with protein accession numbers or determined manually using Gene Ontology (GO) terms generated by Pfam reference numbers.
Genome_build: WCFS1 genome (GenBank accession GCA_000203855.3)
Supplementary_files_format_and_content: Count tables
 
Submission date Jan 22, 2020
Last update date Jan 21, 2022
Contact name Joseph Spangler
Organization name US Naval Research Lab
Street address 4555 Overlook Ave SW
City Washington
State/province DC
ZIP/Postal code 20375
Country USA
 
Platform ID GPL25957
Series (1)
GSE144084 Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-negative pathogen-associated molecule N-3-oxododecanoyl homoserine lactone
Relations
BioSample SAMN13902408
SRA SRX7619590

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

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