|
| Status |
Public on Nov 30, 2021 |
| Title |
invitro_Fp_PEB0191 [Fp-3] |
| Sample type |
SRA |
| |
|
| Source name |
in vitro culture
|
| Organism |
Frischella perrara |
| Characteristics |
strain: PEB0191
treatment: wild type growth in mTYG
Stage: 16 hours of growth
|
| Growth protocol |
Growth in mTYG for 16h; or bee gut colonization for 5 and 10 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol-based RNA extraction
RiboZero rRNA depletion followed by Illumina Truseq library preparation. In vivo samples were depleted of eukaryotic mRNA usig polyA-depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiniSeq |
| |
|
| Data processing |
Trimming for adapters and quality using trimmomatic
For the in vivo: separation of rRNA and non-rRNA reads using sortmerna
Mapping to reference with bowtie2
Generation of count files with HtSeq
Differential gene expression analysis with EdgeR
Genome_build: Reference genome used for read alignment
Supplementary_files_format_and_content: .count files containing counts per gene obtained with HtSeq
|
| |
|
| Submission date |
Nov 28, 2021 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Philipp Engel |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Lausanne
|
| Department |
Department of Fundamental Microbiology
|
| Lab |
https://engelbeelab.com/
|
| Street address |
Biophore Building
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL31006 |
| Series (1) |
| GSE189728 |
RNA sequencing of Frischella perrara |
|
| Relations |
| BioSample |
SAMN23481780 |
| SRA |
SRX13244641 |
