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Sample GSM553708 Query DataSets for GSM553708
Status Public on Jul 24, 2010
Title Roseburia Inulinivorans_starch3_inulin5_B
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) 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 0.743292002 17.97529 18.718582
13A4 0.865631068 15.35602 16.22165107
12I8 0.246721732 16.22358 16.47030173
11A16 0.782967976 15.03554 15.81850798
10I20 0.327839182 14.37411 14.70194918
10A4 0.965963569 15.4703 16.43626357
13M20 0.965915565 15.27968 16.24559557
13E04 0.759470704 15.98972 16.7491907
12M8 0.57493989 16.32657 16.90150989
11E16 0.263403765 15.64342 15.90682376
10M20 -0.241901362 16.02726 15.78535864
10E4 -0.122592601 21.44705 21.3244574
13A24 0.920080094 15.84391 16.76399009
13I4 0.567057449 16.06532 16.63237745
12A12 0.863348664 15.57146 16.43480866
11I16 0.916742497 15.7965 16.7132425
10A24 0.642747182 15.51633 16.15907718
10I4 0.547519009 16.20324 16.75075901
13E24 0.399125879 15.52599 15.92511588
13M4 0.736499939 15.8471 16.58359994

Total number of rows: 4992

Table truncated, full table size 185 Kbytes.




Supplementary file Size Download File type/resource
GSM553708_KS280303i5s3G1.txt.gz 105.4 Kb (ftp)(http) TXT
GSM553708_KS280303i5s3G2.txt.gz 104.5 Kb (ftp)(http) TXT
GSM553708_KS280303i5s3G3.txt.gz 105.7 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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