|
| Status |
Public on Oct 14, 2021 |
| Title |
Rgnavus_Veh_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria culture
|
| Organism |
Mediterraneibacter gnavus |
| Characteristics |
treatment: Vehicle (Ethanol)
strain: Ruminococcus Gnavus ATCC 29149
|
| Treatment protocol |
Exponentially growing culture of R.gnavus were inoculated with vehicle (EtOH) or pregnenolone for 1h.
|
| Growth protocol |
R. gnavus was cultured in anaerobic condition in TSB medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cultures were then stabilized with RNAprotect Bacteria Reagent, then enzymatic lysis (15mg/ml lysozyme) and proteinaseK digestion were performed following manufacturers’ guidelines. RNA was then extracted using RNeasy Mini Kit and on-column DNase treatment was performed following manufacturers’ guidelines.
RNA integrity was checked by agarose gel electrophoresis. Illumina Stranded Total RNA with Ribo Zero Plus was employed with IDT® for Illumina® RNA UD Indexes Set A, for cDNA synthesis and addition of barcode sequences. Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were processed starting from stranded, single ended 75bp-long sequencing reads
Fastq files were generated using BaseSpace tool (Illumina, San Diego, CA, USA). Ruminococcus Gnavus ATCC 29149 genome assembly ASM16947v1 was retrieved from EnsemblBacteria (https://bacteria.ensembl.org) along with the respective gene annotations.
Genome indexes and the subsequent sequencing read alignment were performed using bwa-mem.
Genome_build: genome assembly ASM16947v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 26, 2021 |
| Last update date |
Oct 14, 2021 |
| Contact name |
Andrea Alimonti |
| E-mail(s) |
andrea.alimonti@ior.usi.ch
|
| Organization name |
Institute of oncology research
|
| Department |
Molecular Oncology
|
| Street address |
Via vela 6
|
| City |
Bellinzona |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL30439 |
| Series (1) |
| GSE180863 |
Next Generation Sequencing of Ruminicoccus Gnavus after pregnelonone exposure |
|
| Relations |
| BioSample |
SAMN20409482 |
| SRA |
SRX11556840 |
