|
| Status |
Public on Jun 14, 2023 |
| Title |
RPKM_4h-L-A-PH5_5_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
cell type: bacterial cells
treatment: MRS pH 5.5 (with Lactic acid)
|
| Treatment protocol |
The bacteria was incubated at 30℃ for 4h in MRS media pH 5.5 adjusted pH with HCl or lactic acid
|
| Growth protocol |
Bacteria was cultivated in MRS, MRS media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini kits. 1ug of total RNA was used for the construction of sequencing libraries.
Libraries for Illumina sequencing were made with the TruSeq RNA Library prep kit (Illumina, USA) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends
Sequenced reads were mapped to Lactobacillus_plantarum_WCFS1 (GCF_000203855.3). whole genome by using bowtie v1.1.1 with parameter -I 0 –X 250 -m 1 --chunkmbs 500
The expression level of each cds region was calculated using the reads per kilobase per million mapped reads (RPKM) method.
Assembly: The sequence data for the reference genome was retrieved from the NCBI database (GCF_000203855.3, Lactobacillus plantarum WCFS1).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 19, 2022 |
| Last update date |
Jun 14, 2023 |
| Contact name |
JongHee Lee |
| E-mail(s) |
leejonghee@gmail.com
|
| Organization name |
World Institute of Kimchi
|
| Street address |
kimchi ro86
|
| City |
GwangJu |
| ZIP/Postal code |
61755 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL32583 |
| Series (1) |
| GSE211635 |
Effec of lactic acid or HCl on the Lactiplantibacillus plantarum gene expression |
|
| Relations |
| BioSample |
SAMN30412676 |
| SRA |
SRX17153354 |
