 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
