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Sample GSM2233506 Query DataSets for GSM2233506
Status Public on Feb 16, 2018
Title TAW86, Replicate 3
Sample type RNA
 
Channel 1
Source name TAW86
Organism Bacillus subtilis
Characteristics replication genotype: oriC- oriN+
dnaa, sda, and spo0a genotype: deltadnaA Pspank-sda
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, 40 µg/ml phenylalanine, and 120 µg/ml threonine.
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
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, 40 µg/ml phenylalanine, and 120 µg/ml threonine.
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 1.085265263
2 -0.762784679
3 0.208254804
4 0.621968112
5 1.460080234
6 1.287894434
7 1.226383317
8 -1.679555767
9 -2.610932878
10 -3.343699322
11 -3.854464838
12 -1.123004723
13 1.008059846
14 0.449139538
15 0.196286917
16 0.364583264
17 1.352492804
18 0.219238504
19 1.389507962
20 -0.406288813

Total number of rows: 4624

Table truncated, full table size 77 Kbytes.




Supplementary file Size Download File type/resource
GSM2233506_2011-05-26_9364_bottom_taw86-3.gpr.gz 347.7 Kb (ftp)(http) GPR
Processed data included within Sample table

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