|
| Status |
Public on Mar 02, 2020 |
| Title |
PF2A_ON_Isolate3 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Lacticaseibacillus rhamnosus |
| Characteristics |
strain: GG
growth: Isolate from the overnight culture of the second time fermentation
second time fermentation batch: 2A
freeze-dried batch: NA
growth conditions: Grown in MRS 6.5 broth
|
| Treatment protocol |
No further treatment was applied
|
| Growth protocol |
Freeze-dried product Lactobacillus rhamnosus GG from Chr Hansen were used. Overnight cultures and isolates were grown in MRS pH 6.5-broth and incubated at 37 degrees anaerobically.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using DNeasy Blood & Tissue Minikit (Qiagen)
Eurofins genomics - 4GLI-000100 shotgun library preparation
Eurofins genomics - 4GLI-000100 final quantification of library pool
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Eurofins performed basecalling
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low-quality base pairs (bp) from the reads. The first 5 bps from the 5’end of both paired reads were also trimmed due to the observation of biased quality scores and nucleotide composition.
Spades with the “—careful” setting was used for performing de novo assembly.
Judged by contig coverage distribution, contigs with read coverage lower than 32 folds were removed from downstream analysis
Genome_build: de novo
Supplementary_files_format_and_content: de novo assemblies
|
| |
|
| Submission date |
Dec 12, 2018 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Yun Chen |
| E-mail(s) |
cylsae@gmail.com
|
| Organization name |
Chr Hansen A/S
|
| Department |
Health & Nutrition
|
| Street address |
Bøge Alle 10
|
| City |
Hørsholm |
| ZIP/Postal code |
2970 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL25928 |
| Series (1) |
| GSE123727 |
Lactobacillus rhamnosus GG Genomic and Phenotypic Stability in an Industrial Production Process |
|
| Relations |
| BioSample |
SAMN10585841 |
| SRA |
SRX5126834 |
