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Sample GSM553709 Query DataSets for GSM553709
Status Public on Jul 24, 2010
Title Roseburia Inulinivorans_inulin3_starch5_B
Sample type RNA
 
Channel 1
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 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 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 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) log of Cy3 channel (for base 2)
log2(Cy5) log of Cy5 channel (for base 2)

Data table
ID_REF VALUE log2(Cy3) log2(Cy5)
13I20 0.000577599 21.39986 21.4004376
13A4 -0.878034651 16.17169 15.29365535
12I8 0.266615052 14.96137 15.22798505
11A16 -0.611408832 15.28127 14.66986117
10I20 -1.260474771 18.18998 16.92950523
10A4 -1.60671735 19.43334 17.82662265
13M20 -1.318244392 17.11471 15.79646561
13E04 -0.936369453 17.10044 16.16407055
12M8 0.33353764 19.30139 19.63492764
11E16 -2.219701921 17.72205 15.50234808
10M20 -0.099615275 14.78321 14.68359473
10E4 -0.380108261 20.20669 19.82658174
13A24 -1.389227023 15.30693 13.91770298
13I4 -0.589974526 15.87315 15.28317547
12A12 -1.712596347 16.38986 14.67726365
11I16 -1.410135357 15.91244 14.50230464
10A24 -0.193575031 15.22603 15.03245497
10I4 -0.564223965 18.05994 17.49571604
13E24 0.433142822 13.93821 14.37135282
13M4 -0.24552786 17.70259 17.45706214

Total number of rows: 4992

Table truncated, full table size 185 Kbytes.




Supplementary file Size Download File type/resource
GSM553709_KS280303s5i3G1.txt.gz 104.8 Kb (ftp)(http) TXT
GSM553709_KS280303s5i3G2.txt.gz 105.0 Kb (ftp)(http) TXT
GSM553709_KS280303s5i3G3.txt.gz 107.2 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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