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Sample GSM553706 Query DataSets for GSM553706
Status Public on Jul 24, 2010
Title Roseburia Inulinivorans_inulin3_starch5_A
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 -0.765793325 21.79294 21.02714668
13A4 1.254375348 15.57824 16.83261535
12I8 1.195846839 15.54824 16.74408684
11A16 0.666277916 15.07922 15.74549792
10I20 2.178462121 14.00913 16.18759212
10A4 0.184612015 16.75388 16.93849202
13M20 -1.749579348 17.00352 15.25394065
13E04 -0.36558948 16.59096 16.22537052
12M8 -0.859928097 20.08351 19.2235819
11E16 1.271723261 15.96612 17.23784326
10M20 0.677065276 15.33053 16.00759528
10E4 -2.213693779 20.94001 18.72631622
13A24 1.37153988 15.14037 16.51190988
13I4 2.206155118 14.93609 17.14224512
12A12 -0.866013638 15.96438 15.09836636
11I16 0.935585101 15.03076 15.9663451
10A24 0.721701952 15.57766 16.29936195
10I4 -0.622588261 18.97106 18.34847174
13E24 0.028427263 15.30381 15.33223726
13M4 -0.259064277 16.93479 16.67572572

Total number of rows: 4992

Table truncated, full table size 185 Kbytes.




Supplementary file Size Download File type/resource
GSM553706_KS280203i3s5G1.txt.gz 106.1 Kb (ftp)(http) TXT
GSM553706_KS280203i3s5G2.txt.gz 105.0 Kb (ftp)(http) TXT
GSM553706_KS280203i3s5G3.txt.gz 107.0 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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