|
| Status |
Public on Apr 21, 2020 |
| Title |
GHU-61: Pool7 of 10 genomic DNA sample from dcshA cold-suppressor strains |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: SA564
tissue: bacterial culture
pool_size: 10
|
| Growth protocol |
Suppressors strains where selected by platting 50 μl of ON cultures of DcshA strain grown at 37°C in MH medium on MH plate at 25°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
kit QIAGEN dnEasy blood and tissue kit
Genomic Library were prepared by the service provider Fasteris SA (Switzerland) following the protocol TruSeq Nano DNA Library Prep.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The source code use to process the data is available here: https://gitlab.unige.ch/LinderLab/evar
filter low quality reads and trim adapter sequence with "SGA preprocess"
filter reads containing sequencing errors with "SGA filter"
perfom k-mer counting with "SGA kmer-count" considering kmer size of 61nt
perform de novo assembly of contigs with "SGA fm-merge" considering kmer size of 61nt
compute assemlby graph with "SGA overlap"
identify contigs containing k-mers not seen in the reference genome. This are candidates containing mutations
map contigs onthe reference genome for annotation only (not for mutation detection)
Manual curration of the identified mutations
Genome_build: S. aureus strain SA564, Refseq assembly: GCF_001281145.1
Supplementary_files_format_and_content: A table in TSV format (Tab Separated Value) listing manualy curated mutations identified in the sequencing data
|
| |
|
| Submission date |
Jun 19, 2019 |
| Last update date |
Apr 21, 2020 |
| Contact name |
Julien Prados |
| E-mail(s) |
julien.prados@unige.ch
|
| Phone |
+41 22 37 95 396
|
| Organization name |
University of Geneva
|
| Department |
SCMU
|
| Lab |
Bioinformatics Support Platform
|
| Street address |
Rue Michel Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19006 |
| Series (1) |
| GSE133013 |
The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN12096233 |
| SRA |
SRX6095253 |
