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Sample GSM2233493 Query DataSets for GSM2233493
Status Public on Feb 16, 2018
Title TAW5 +HPUra, Replicate 3
Sample type RNA
 
Channel 1
Source name TAW5
Organism Bacillus subtilis
Characteristics replication genotype: oriC- oriN+
dnaa, sda, and spo0a genotype: Pspank-dnaA
Treatment protocol HPUra was added to a final concentration of 38 µg/ml, and cells were harvested 1 hour later
Growth protocol Cells were grown to mid-log phase in batch culture at 37 °C in minimal media supplemented with 1% (w/v) arabinose, 0.5% (w/v) xylose, 0.1 mM IPTG, 40 µg/ml tryptophan, and 40 µg/ml phenylalanine.
Extracted molecule total RNA
Extraction protocol Cultures were fixed with an equal volume of -20C methanol. RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.
Label Cy5
Label protocol 10 µg of each RNA sample was reverse transcribed using Superscript II reverse transcriptase (Invitrogen), random hexamers, and aminoallyl-dUTP (Ambion). The cDNA was labeled by conjugation to monofunctional Cy3 or Cy5 dyes (Amersham) for reference or experimental samples, respectively. Each experimental sample was mixed with an aliquot of reference sample.
 
Channel 2
Source name Reference RNA
Organism Bacillus subtilis
Characteristics reference rna: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352
Treatment protocol HPUra was added to a final concentration of 38 µg/ml, and cells were harvested 1 hour later
Growth protocol Cells were grown to mid-log phase in batch culture at 37 °C in minimal media supplemented with 1% (w/v) arabinose, 0.5% (w/v) xylose, 0.1 mM IPTG, 40 µg/ml tryptophan, and 40 µg/ml phenylalanine.
Extracted molecule total RNA
Extraction protocol Cultures were fixed with an equal volume of -20C methanol. RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.
Label Cy3
Label protocol 10 µg of each RNA sample was reverse transcribed using Superscript II reverse transcriptase (Invitrogen), random hexamers, and aminoallyl-dUTP (Ambion). The cDNA was labeled by conjugation to monofunctional Cy3 or Cy5 dyes (Amersham) for reference or experimental samples, respectively. Each experimental sample was mixed with an aliquot of reference sample.
 
 
Hybridization protocol Salmon testes DNA and yeast tRNA were added, and each cDNA sample was hybridized to a DNA microarray at 42 °C overnight.
Scan protocol Scanned on a GenePix 4000B scanner. Images were quantified using GenePix 3.0 (Axon Instruments).
Data processing Loess normalized and background subtracted using the R statistical software package Linear Models for Microarray Data (LIMMA). [RGbkgd <- backgroundCorrect(RG, method=normexp, offset=50); normalizeWithinArrays(RGbkgd)]
 
Submission date Jul 14, 2016
Last update date Feb 16, 2018
Contact name Alan Grossman
E-mail(s) adg@mit.edu
Organization name MIT
Department Biology
Street address 31 Ames St.
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL10707
Series (1)
GSE84421 Expression profiles of Bacillus subtilis strains deleted for or ectopically expressing dnaA, sda, and spo0A during exponential growth and after treatment with HPUra.

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 0.155894121
2 -0.38538089
3 0.137254187
4 0.282820216
5 -0.052604512
6 -0.0313701
7 1.306812874
8 -1.579568654
9 -0.674997259
10 -0.634508123
11 -0.514020028
12 -0.362147714
13 0.013531958
14 0.146788013
15 -0.077799942
16 0.063488925
17 0.309754555
18 0.224844255
19 -0.050458232
20 0.474073667

Total number of rows: 4624

Table truncated, full table size 77 Kbytes.




Supplementary file Size Download File type/resource
GSM2233493_062508_wgs9-404_top_+HPUra_TAW5.gpr.gz 337.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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