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Sample GSM624445 Query DataSets for GSM624445
Status Public on Oct 10, 2012
Title TC01 bile_3
Sample type RNA
Source name Cultured cells
Organism Lacticaseibacillus casei
Characteristics agent: bile
strain: TC01. L. casei BL23 with a complete deletion of gene LCABL_02080.
Treatment protocol Cells were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The culture was then two fold diluted with prewarmed MRS medium supplemented with 0.2% bovine bile (Sigma) and incubation continued for 45 min.
Growth protocol Cells were stored at -80C in MRS medium supplemented with 15% glycerol (stock culture). For the assay, cells from the stock culture were inoculated in MRS agar plates. A single colony was used to inoculate 5 ml of MRS medium and the culture was incubated overnight at 37C. This culture was used to inoculate MRS medium at 0.05 O.D. 595 nm. for the treatment or control assays.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from L. casei by using TRIZOL reagent (Invitrogen). Cells were collected by centrifugation, washed with cold 50 mM EDTA (pH 8.0), resuspended in 1 ml of TRIZOL reagent, and then mechanically disrupted with glass beads in a cell disrupter (Savant Instruments, Holbrook, N.Y.). Additional steps were performed according to the instructions of the TRIZOL manufacturer. RNA samples purified as described above were treated with the Ambion Turbo DNA-free kit (Applied Biosystems) using the routine DNase I treatment outlined by the supplier in order to remove contaminating DNA. The quality and concentration of the RNA samples were subsequently evaluated by using the Experion automated electrophoresis system (Bio-Rad). Samples with 23S/16S ratios lower than 0.85 were discarded.
Label 33P-dCTP
Label protocol First-strand cDNA was synthesized from 45 µg RNA using the Transcriptor first strand cdna synthesis kit (Roche) with random hexamer primers as recommended by the manufacturer. Labelled cDNA was purified with illustra MicroSpin G-50 Columns (GE Healthcare) as recommended by the manufacturer.
Hybridization protocol SDS based hybridization solution, during 24 hours
Scan protocol FUJIFILM FLA-3000
Data processing The software for image analysis is ArrayVision 7.0 (Imaging Research Inc.). This software yields raw and background substracted data.
The Background Substracted Signals are raw individual data. After considering the three replicates performed in the experiment and after median normalization, first between replicates and after between conditions, we obtain the ratio values for each gene/ORF (see supplementary file on Series record).
Submission date Nov 17, 2010
Last update date Oct 10, 2012
Contact name Manuel Zúñiga
Phone 34 963900022
Fax 34 963636301
Organization name Instituto de Agroquímica y Tecnología de Alimentos
Department Biotecnología
Lab Bacterias lácticas y Probióticos
Street address Avda. Profesor Agustín Escardino 7
City Paterna
State/province Valencia
ZIP/Postal code 46980
Country Spain
Platform ID GPL11074
Series (1)
GSE25448 Comparison of the response to bile of Lactobacillus casei BL23 and its derivative strain TC01

Data table header descriptions
TC01 bile-3 Raw signal for L. casei TC01 strain grown in MRS medium supplemented with bile replicate 3
VALUE Background substracted signal

Data table
ID_REF TC01 bile-3 VALUE
R1 - C1 : 1 127.06 115.657
R1 - C1 : 2 122.65 111.247
R1 - C1 : 3 52.5 41.102
R1 - C2 : 1 133.16 122.521
R1 - C2 : 2 21.89 11.247
R1 - C2 : 3 62.67 52.029
R1 - C3 : 1 211.66 200.817
R1 - C3 : 2 307.51 296.664
R1 - C3 : 3 35.39 24.544
R1 - C4 : 1 148.99 137.618
R1 - C4 : 2 21.5 10.127
R1 - C4 : 3 94.51 83.136
R1 - C5 : 1 124.04 115.194
R1 - C5 : 2 18.34 9.496
R1 - C5 : 3 10.09 1.245
R1 - C6 : 1 103.08 92.224
R1 - C6 : 2 18.12 7.27
R1 - C6 : 3 106.53 95.679
R1 - C7 : 1 290.47 279.479
R1 - C7 : 2 29.32 18.33

Total number of rows: 2688

Table truncated, full table size 67 Kbytes.

Supplementary data files not provided
Processed data are available on Series record

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