|
| Status |
Public on Dec 07, 2016 |
| Title |
2.3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Propionibacterium freudenreichii |
| Characteristics |
strain: CIRM-BIA 138 alias ITG P20
growth phase: stationary
|
| Treatment protocol |
Bacterial cells were recovered by a centrifugation step and incubated into RNA protect (Qiagen).
|
| Growth protocol |
Planktonic culture in Yeast Extract Lactate medium (Malik) grown under microaerophilic conditions at 30°C without addition of any nutrient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy Mini Kit (Qiagen) and Dnase treatment. Ribosomic RNA were depleted using Ribozero for Gram plus (Epicentre). Quality was checked using Nanodrop and Nanochips for Bioanalyseur (Agilent).
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA from stationary growth phase 6
|
| Data processing |
Libraries were sequenced on an Illumina HiSeq 2000 as 50 pb reads using the Sequence By Synthesis technique at the Montpellier GenomiX facility.
Image analyses and basecalling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
reads were mapped using bowtie
mapped reads were counted using htseq-count with union parameter
Genome_build: GCA_000945235.1
Supplementary_files_format_and_content: Tab-delimited file with a first column for gene identification. The next columns correspond to the gene counts for each sample.
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hélène Falentin |
| E-mail(s) |
helene.falentin@rennes.inra.fr
|
| Organization name |
INRA
|
| Department |
Microbiologie
|
| Lab |
UMR STLO
|
| Street address |
65 rue de St Brieuc
|
| City |
Rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
| |
|
| Platform ID |
GPL21193 |
| Series (1) |
| GSE75553 |
Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage |
|
| Relations |
| BioSample |
SAMN04304516 |
| SRA |
SRX1457522 |
