|
| Status |
Public on Oct 27, 2020 |
| Title |
pH55_2 |
| Sample type |
SRA |
| |
|
| Source name |
3h after MRS pH 5.5 rep2
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
treatment: 3h after MRS pH 5.5
|
| Treatment protocol |
Bacteria was cultivated until OD600 =0.5 and treated with MRS pH 5.5 or MRS pH 5.0
|
| Growth protocol |
Bacteria was cultivated with MRS media (pH 6.2)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted and purified using the Bacterial RNA kit (qiagen) according to the protocol provided by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
kimchi origin
|
| Data processing |
bcl2fastq 1.8.4 software combines per-cycle BCL basecall files that generated Illumina sequencing instruments and translates them into FASTQ files. The raw FASTQ files were split into files containing about 20,000,000 reads and checked for quality using the FASTQC (v0.11.7). The reads were filtered (removing sequences that did not pass Illumina's quality filter) and trimmed based on the quality results by trimmomatic-0.36. Quality filtered reads were aligned to the reference-genome sequence using Bowtie2 (v 2.2.3). The sequence data for the reference genome was retrieved from the NCBI database (GCF_000203855.3, Lactobacillus plantarum WCFS1) . Qualityfiltered reads were aligned to the reference-genome sequence using Bowtie2. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM). The eggNOG (evolutionary genealogy of genes: Nonsupervised Orthologous Groups) database was used to cluster genes into functionally related groups and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used to analyze metabolic pathway.
Genome_build: Lactobacillus plantarum WCFS1 (CGF_000203855.3)
Supplementary_files_format_and_content: normalized counts
|
| |
|
| Submission date |
Jan 16, 2020 |
| Last update date |
Oct 27, 2020 |
| Contact name |
JongHee Lee |
| E-mail(s) |
leejonghee@gmail.com
|
| Organization name |
WIKIM
|
| Department |
Advanced Process Technology and Fermentation Research Group
|
| Street address |
kimchiro 86
|
| City |
GwangJu |
| State/province |
GwangJu |
| ZIP/Postal code |
61755 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL23496 |
| Series (1) |
| GSE143834 |
Characterization of Lactobacillus plantarum gene expression in the acidic conditions |
|
| Relations |
| BioSample |
SAMN13874348 |
| SRA |
SRX7573348 |
