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Sample GSM978056 Query DataSets for GSM978056
Status Public on Aug 03, 2012
Title RpoHII replicate 3
Sample type RNA
 
Source name Gene expression levels in R. sphaeroides expressing RpoHII
Organism Cereibacter sphaeroides 2.4.1
Characteristics strain: RSP_0601 mutant with plasmid containing RpoHII
growth phase: mid-eponential
grow conditions: aerobic in minimal medium
Treatment protocol Cell culture was transferred to an ice-cold conical tube containing 1/8 volume of 5% water-saturated phenol in ethanol. Cells were collected by centrifugation (5,000 X g for 5 min at 4 C); cell pellets were frozen in dry ice/ethanol and stored at -80 C.
Growth protocol Cells were cultured in minimal succinate based medium under aerobic conditions at 30C until early-exponential growth phase when 100 uM IPTG was added to induce the expression of RpoHI_FLAG for 3 hours before harvesting cells.
Extracted molecule total RNA
Extraction protocol Cells were lysed by addition of 1/10 v 10% SDS at 64 C for 2 min. 1/10 v 1 M Na acetate (pH 5.2), then equal volume of H2O-saturated phenol, were added. Samples were incubated at 64 C for 6 min, with mixing every 30 s, then chilled on ice before centrifugation (16,000 X g for 10 min at 4 C). The aqueous phase was removed and extracted with equal volumes of phenol, then chloroform, then precipitated (1/10 v 3 M Na acetate, 1 mM EDTA, 2 volumes cold ethanol).
Label biotin
Label protocol Fragmented cDNA was end-labeled with biotin-16-ddUTP using Terminal Transferase for 2 hr at 37 C.
 
Hybridization protocol Labeled cDNA samples were hybridized to Rhodobacter sphaeroides GeneChip CustomExpress microarrays (Affymetrix) following product instructions, for 16 h at 45 C on a rotisserie spindle rotating at 60 rpm.
Scan protocol Microarrays were washed, stained, and scanned using the Pseudomonas aeruginosa midi-array hybridization with amplification protocols.
Data processing Microarray data sets were normalized by Robust Multichip Average (RMA) with background adjustment and quantile normalization. Statistical analysis of normalized data to identify differentially expressed genes used the limma package. Correction for multiple testing was done using Benjamini-Hochberg correction. Differentially expressed genes were defined as those having an adjusted p-value ≤ 0.01 and a fold-change ≥ 2 with respect to those in the reference data sets. All analyses were conducted in the R statistical programming environment (http://www.R-project.org).
 
Submission date Jul 29, 2012
Last update date Aug 03, 2012
Contact name Yann S Dufour
Organization name University of Wisconsin - Madison
Department Bacteriology
Lab Timothy Donohue
Street address 1550 Linden Drive
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL162
Series (2)
GSE39712 RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from gene expression profiling
GSE39806 RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1

Data table header descriptions
ID_REF
VALUE log2 expression signal (rma normalized)

Data table
ID_REF VALUE
1 6.096475908
2 6.424618116
3 5.508445898
4 5.77490465
5 5.516016982
6 5.230782769
7 5.780898824
8 5.921063243
9 5.279183901
10 5.576871965
11 5.102657526
12 5.297225585
13 5.143246367
14 5.189309566
15 4.995208219
16 4.954781656
17 5.103575921
18 5.397474454
19 4.972134308
20 4.963431514

Total number of rows: 5355

Table truncated, full table size 87 Kbytes.




Supplementary file Size Download File type/resource
GSM978056_RpoHII_rep_3.CEL.gz 774.4 Kb (ftp)(http) CEL
Processed data included within Sample table

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