|
| Status |
Public on Feb 13, 2021 |
| Title |
invitro_MIX_PE_3 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro culture
|
| Organisms |
Lactobacillus apis; Lactobacillus kullabergensis; Lactobacillus helsingborgensis; Lactobacillus melliventris |
| Characteristics |
phylotype: Lactobacillus Firm5
treatment: Pollen extract
strain: Community (mixture of all species)
Stage: 16 hours post-inoculation
|
| Growth protocol |
For the in vitro samples: bacteria were grown in basal medium supplemented with either glucose (G) or pollen extract (PE) for 16 hours at 34˚C in anarobic conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the in vivo samples: bacteria were harvested from rectums of bees that were fed with sugar water + pollen grains (SWPG) or with sugar water (SW) only 5 days post-colonization
For the in vitro samples libraries were prepared following the protocol published in Nature Protocols by Avraham et al. (2016). For the in vivo samples libraries were prepared using the Zymo-Seq RiboFree Total RNA Library kit (Zymo Research).
|
| |
|
| 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: Lapi = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029476.1
Genome_build: Lhel = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029544.1
Genome_build: Lmel = https://www.ncbi.nlm.nih.gov/nuccore/NZ_QGLG00000000.1
Genome_build: Lkul = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029477.1
Supplementary_files_format_and_content: .count files containing counts per gene obtained with HtSeq
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Feb 14, 2021 |
| Contact name |
Silvia Brochet |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Lausanne
|
| Department |
Department of Fundamental Microbiology
|
| Lab |
Engel
|
| Street address |
UNIL campus, Biophore building
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL29724 |
| Series (1) |
| GSE166724 |
Lactobacillus Firm5 in vivo and in vitro RNA sequencing |
|
| Relations |
| BioSample |
SAMN17904063 |
| SRA |
SRX10092737 |
