|
| Status |
Public on Oct 14, 2022 |
| Title |
GR1008 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria culture
|
| Organism |
Limosilactobacillus fermentum |
| Characteristics |
strain: GR1008
|
| Growth protocol |
The bacterial culture was struck out on MRS agar plate and incubated anaerobically at 37oC for 48 h. The bacterial cells were scraped from the agar plate and dissolved in designated buffer for further experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA preparation was carried out using TRIzol Max Bacterial RNA Isolation Kit (Thermofisher, MA, USA) following manufacturer’s instructions.
The rRNA was then depleted from extracted RNA and the cDNA library was synthesized using random primers. The library was ligated with adaptors and filtered according to molecular weight
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument for base calling
Cutadapt (v1.9.1) for quality control
Bowtie2 (v2.2.6) for mapping
HT-seq (v0.6.1) for calculation of fragments per kilobases per million reads (FPKM)
DESeq (v1.38.0) for differential analysis
Genome_build: GenBank ID: CP071000.1
Supplementary_files_format_and_content: Matrix table with gene annotations, counts, and FPKM
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Oct 14, 2022 |
| Contact name |
Hsu-Feng Chu |
| E-mail(s) |
cv47richy@gmail.com
|
| Organization name |
National Yang-Ming-Chiao-Tung university
|
| Street address |
No.155, Sec.2, Linong Street
|
| City |
Taipei |
| ZIP/Postal code |
112-21 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL30868 |
| Series (1) |
| GSE186000 |
Total RNAseq of Lactobacillus fermentum |
|
| Relations |
| BioSample |
SAMN22328875 |
| SRA |
SRX12633412 |
