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Sample GSM553707 Query DataSets for GSM553707
Status Public on Jul 24, 2010
Title Roseburia Inulinivorans_starch3_inulin5_A
Sample type RNA
 
Channel 1
Source name mRNA extracted from Roseburia Inulinivorans grown on starch at OD 0.4
Organism Roseburia inulinivorans DSM 16841
Characteristics strain: A2-194
Growth protocol Routine anaerobic culturing of R. inulinivorans A2-194 was in M2GSC medium (39). Growth on single carbon sources utilised basal YCFA medium (3) supplemented with 0.5 % w/v of the specific substrate (amylopectin starch, Sigma).
Extracted molecule total RNA
Extraction protocol RNA was purified from mid-exponential phase (OD650 = 0.4) cultures on basal YCFA supplemented with starch using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion).
Label Cy3
Label protocol The purified RNA (1 ug) was labelled by reverse transcription (Amersham Cyscribe first-strand cDNA labelling kit), employing random nonamer extension incorporating either dCTP-Cy3 dye.
 
Channel 2
Source name mRNA extracted from Roseburia Inulinivorans grown on inulin at OD 0.4
Organism Roseburia inulinivorans DSM 16841
Characteristics strain: A2-194
Growth protocol Routine anaerobic culturing of R. inulinivorans A2-194 was in M2GSC medium (39). Growth on single carbon sources utilised basal YCFA medium (3) supplemented with 0.5 % w/v of the specific substrate (inulin -Dahlia, Sigma).
Extracted molecule total RNA
Extraction protocol RNA was purified from mid-exponential phase (OD650 = 0.4) cultures on basal YCFA supplemented with inulin using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion).
Label Cy5
Label protocol The purified RNA (1 ug) was labelled by reverse transcription (Amersham Cyscribe first-strand cDNA labelling kit), employing random nonamer extension incorporating dCTP-Cy5 dye.
 
 
Hybridization protocol Hybridization was done in the GeneTAC hybridization station (Genomic Solutions) with agitation and using circulating buffers. Slides were first blocked in buffer (180mM succinic anhydride, 44mM sodium borate in 1-methyl-2-pyrrolidone), washed in deionised water at 98°C (2× 1min) and finally in 95 % ethanol (1 min) at room temperature. After drying the slides were pre-hybridized at 50°C for 30 min (in 10 mg ml17 fraction V BSA, 3.5× SSC and 0.1% SDS), washed again in deionised water, dried and immediately hybridized. The hybridization solution (labelled cDNA mixed with 10µg Human Cot-1 DNA (Invitrogen), 15.4 µg yeast tRNA, 8 µl poly dA, 14.4 µl 20× SSC and 2.4 µl 100× Denhardt’s solution) was first boiled for 2 min and cooled to 45°C before adding 1.4 µl 5% SDS and incubating at 65°C for 30 min. This solution was then added to the array slides which were hybridized for 16 h at 65°C before washing at room temperature in medium stringency buffer (0.1 % SDS, 0.5× SSC) for 5 min, followed by two high stringency washes (0.1 % SDS, 0.1× SSC) of 5 min each.
Scan protocol The fluorescence of each spot was measured in two channels using a GeneTAC LS IV (Genomic Solutions) utilising GeneTac Integrator version 3.0.1 software.
Description Strain Roseburia inulinivorans A2-194 was isolated from a human faecal sample in 1997, and is a member of the Firmicutes
Data processing The microarray data were log2-transformed and normalised by Loess normalisation to remove intensity dependent dye-effects. As each clone was represented by three spots we calculated the median of the three log2(Cy5/Cy3) values, a robust measure of relative gene expression. In total the fluorescence of 12 hybridising spots were compared for each clone. P-values were calculated by applying a one-sample t-test to the two log-ratios from the two replicate experiments, while the two dye-swapped arrays within each experiment were combined by averaging.
 
Submission date Jun 09, 2010
Last update date Jul 23, 2010
Contact name Gill Campbell
E-mail(s) G.Campbell@abdn.ac.uk
Phone +44 (0) 1224 716627
Fax +44 (0) 1224 716647
URL http://www.rowett.ac.uk
Organization name University of Aberdeen
Department Rowett Institute of Nutrition and Health
Street address Greenburn Road
City Aberdeen
ZIP/Postal code AB21 9SB
Country United Kingdom
 
Platform ID GPL10020
Series (1)
GSE22245 Differential gene expression in Roseburia inulinivorans grown on inulin and starch

Data table header descriptions
ID_REF
VALUE log2(Cy5)-log2(Cy3)
log2(Cy3) log2 of Cy3
log2(Cy5) log2 of Cy5

Data table
ID_REF VALUE log2(Cy3) log2(Cy5)
13I20 1.890620026 16.14372 18.03434003
13A4 2.15626878 15.07655 17.23281878
12I8 1.947664134 15.61446 17.56212413
11A16 1.494134595 15.82068 17.31481459
10I20 1.026618436 15.01195 16.03856844
10A4 1.659429917 15.27557 16.93499992
13M20 2.147072802 15.33451 17.4815828
13E04 1.746579601 15.37319 17.1197696
12M8 2.759461588 14.58951 17.34897159
11E16 2.307956175 15.11657 17.42452618
10M20 1.262825381 16.36229 17.62511538
10E4 0.525472453 21.70685 22.23232245
13A24 1.950595039 15.857 17.80759504
13I4 2.540136596 15.56031 18.1004466
12A12 2.886476878 15.13228 18.01875688
11I16 2.290261506 15.05404 17.34430151
10A24 2.384458519 15.65063 18.03508852
10I4 2.124780379 15.66747 17.79225038
13E24 2.858980222 15.44164 18.30062022
13M4 2.760280814 14.79035 17.55063081

Total number of rows: 4992

Table truncated, full table size 185 Kbytes.




Supplementary file Size Download File type/resource
GSM553707_KS280203i5s3G1.txt.gz 104.6 Kb (ftp)(http) TXT
GSM553707_KS280203i5s3G2.txt.gz 103.0 Kb (ftp)(http) TXT
GSM553707_KS280203i5s3G3.txt.gz 104.9 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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