|
| Status |
Public on Dec 19, 2018 |
| Title |
2m7b |
| Sample type |
SRA |
| |
|
| Source name |
culture
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: WCSF1
time: 4 h
|
| 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 |
| |
|
| Description |
rpkm_0_ADTV7.txt
rpkm_1_ADTV7.txt
rpkm_2_ADTV7.txt
rpkm_3_ADTV7.txt
|
| Data processing |
Generated MiSeq reads were then analyzed via the RNAseq pipeline described by Li et al. (Li et al., 2018).
Read quality control was performed where Phred scores of <20 were trimmed using FastQC and Cutadapt as part of Trim Galore! (Krueger, 2015)
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) (Magoc et al., 2013) for paired end reads was used with default settings on the remaining reads for alignment to the L. plantarum WCFS1 genome from NCBI (ftp://ftp.ncbi. nih.gov/genomes/Bacteria) generating RPKM files and count tables.
Each count table was read into R where DESeq2 (Love et al., 2014) was used for differential expression analysis and generating associated statistics as a function of treatment with 3OC12 and time.
Supplementary_files_format_and_content: Count tables
Supplementary_files_format_and_content: counts for all genes in files that begin with rpkm_0
|
| |
|
| Submission date |
Dec 18, 2018 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Scott Nathan Dean |
| E-mail(s) |
scottnathandean@gmail.com
|
| Organization name |
Naval Research Laboratory
|
| Street address |
4555 Overlook Ave SW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20375 |
| Country |
USA |
| |
|
| Platform ID |
GPL25957 |
| Series (1) |
| GSE124050 |
Response of Lactobacillus plantarum WCSF1 to the Gram-negative pathogen-associated quorum sensing molecule N-3-oxododecanoyl homoserine lactone. |
|
| Relations |
| BioSample |
SAMN10612065 |
| SRA |
SRX5160597 |
