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Sample GSM864335 Query DataSets for GSM864335
Status Public on Jan 02, 2013
Title prsW mutant_rep1
Sample type RNA
 
Source name prsW mutant
Organism Bacillus subtilis subsp. subtilis str. 168
Characteristics genotype/variation: prsW mutant
Growth protocol B. subtilis 168 and respective mutants were grown in Luria Bertani broth O.D. 600nm 1.0
The complete description of the growth protocols can be found in Zweers et al., to be submitted.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).
 
Hybridization protocol Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.
Description growth in LB medium_O.D. 600nm 1.0
prsW_1
Data processing An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).
 
Submission date Jan 20, 2012
Last update date Jan 02, 2013
Contact name Emma L Denham
E-mail(s) e.l.denham@warwick.ac.uk
Organization name University of Warwick
Department Warwick Medical School
Lab Division of Microbiology and Infection
Street address Gibbet Hill Road
City Coventry
ZIP/Postal code CV4
Country United Kingdom
 
Platform ID GPL15150
Series (1)
GSE35236 Definition of the σ(W) Regulon of Bacillus subtilis in the Absence of Stress

Data table header descriptions
ID_REF
VALUE quantile-normalized gene-level intensity

Data table
ID_REF VALUE
1 7.829765625
2 8.783825
3 14.51725
4 8.95090625
5 13.37536875
6 13.639121875
7 13.451975
8 12.804090625
9 13.319853125
10 13.44060625
11 13.2768875
12 12.849984375
13 13.6304625
14 14.338803125
15 10.10536875
16 7.456721875
17 15.017459375
18 8.093015625
19 13.94858125
20 14.486203125

Total number of rows: 5737

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM864335_34115402_01_532.pair.gz 7.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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