|
| Status |
Public on Jun 13, 2017 |
| Title |
CIRM456-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Propionibacterium freudenreichii CIRM-BIA 456 wild-type
|
| Organism |
Propionibacterium freudenreichii |
| Characteristics |
strain: Propionibacterium freudenreichii CIRM-BIA 456
genbank assembly: GCA_001369075.1
|
| Growth protocol |
Growth on skim cow milk ultrafiltrat supplemented with sodium L-lactate and casein hydrolysate for 72h, at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was performed as previously described for Propionibacterium freudenreichii (Saraoui, et al. 2013) using Rneasy Mini Kit (Qiagen, Germany) and a subsequent DNase treatment (Dnase Rnase free, Ambion) according to the supplier. RNA concentrations were quantified using a Nanodrop. RNA quality (RIN) was evaluated using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Retrotranscriptions, labelings, hydridizations and scans of the microarrays were then performed by the GeT-PlaGe platform (Genotoul, Toulouse, France). RNA were retrotranscribed into double stranded DNA using Superscript Double Strand cDNA Synthesis Kit (Invitrogen). The ratios 260/230 and 260/280 were greater than 1.8 and the concentrations greater than 150 ng/μl. According to the recommendations of the supplier, double stranded DNAs were labeled using One Color DNA Labeling (NimbleGen, Roche Diagnostics, France).
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| |
|
| Hybridization protocol |
Hybridizations were carried out using the NimbleGen Hybridization Kit and the Sample Tracking Control Kit (NimbleGen, Roche Diagnostics, France).
|
| Scan protocol |
Hybridized microarrays were scanned using a MS200 scanner (Roche Diagnostics, France) with a resolution of 5 µm.
|
| Description |
Propionibacterium freudenreichii strain CIRM456 grown on supplemented cow milk ultrafiltrat, biological replicate 2.
|
| Data processing |
The processing of the microarray data relied on custom Perl and R scripts. In our design, template probes were derived into perfect match variants capturing the allelic variations in the 8 genome. For each strain we retained only the intensity measurements obtained with the perfect match probes. Measured intensities of the probes corresponding to the core genome (1345 genes) where quantile normalized towards a reference distribution obtained as a median over 16 hybridizations. The transformation specific to each array adjusted on the core genome was then also applied to the variable gene pool. For each hybridization, we computed an aggregated expression index for each gene in the corresponding strain as a median of the normalized intensities for the perfect match probes. After visual quality check based on the distribution of probe intensities, most strains were represented by two biological replicates (1 for CIRM 134, 3 for CIRM 514 and 516).
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| |
|
| Submission date |
Oct 03, 2016 |
| Last update date |
Jun 13, 2017 |
| Contact name |
Pierre Nicolas |
| E-mail(s) |
pierre.nicolas@inrae.fr
|
| Phone |
+33-1-3465-2894
|
| Organization name |
INRAE - Université Paris-Saclay
|
| Lab |
MaIAGE
|
| Street address |
INRAE - Domaine de Vilvert
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
F-78350 |
| Country |
France |
| |
|
| Platform ID |
GPL22522 |
| Series (1) |
| GSE87574 |
Transcriptome profiling of Propionibacterium freudenreichii strains associated with different anti-inflammatory properties. |
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