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Sample GSM1881351 Query DataSets for GSM1881351
Status Public on Feb 02, 2016
Title L1_50B over L1_90A
Sample type RNA
 
Channel 1
Source name L1_50B
Organism Bacillus cereus ATCC 14579
Characteristics strain: ATCC 14579
treatment: heat-treated spores 50 min after mixing with BHI
Treatment protocol Cells were harvested at above mentioned timepoints (see overall design) by spinning down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen.
Growth protocol Untreated and heat-treated (1 min 95C) B. cereus ATCC14579 spores were mixed with BHI and incubated with aeration (200rpm) at 30°C untill harvesting time (see overal design).
Extracted molecule total RNA
Extraction protocol RNA was extracted from samples in TRI-reagent by defrosting on ice, spores were mechanically disrupted by extensive bead beating in the presence of Lysing Matrix B beads. Direct-zol RNA MiniPrep was used according to the manufacturer’s instructions for on column RNA purification. Residual chromosomal DNA was removed by 30 min off column treatment of the samples with TURBO DNA-free Kit. The resulting mRNA was subsequently cleaned with RNeasy Mini Kit. The RNA quantity and quality were checked by UV spectroscopy and RNA 6000 Nanochip.
Label cy5
Label protocol Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)
 
Channel 2
Source name L1_90A
Organism Bacillus cereus ATCC 14579
Characteristics strain: ATCC 14579
treatment: heat-treated spores 90 min after mixing with BHI
Treatment protocol Cells were harvested at above mentioned timepoints (see overall design) by spinning down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen.
Growth protocol Untreated and heat-treated (1 min 95C) B. cereus ATCC14579 spores were mixed with BHI and incubated with aeration (200rpm) at 30°C untill harvesting time (see overal design).
Extracted molecule total RNA
Extraction protocol RNA was extracted from samples in TRI-reagent by defrosting on ice, spores were mechanically disrupted by extensive bead beating in the presence of Lysing Matrix B beads. Direct-zol RNA MiniPrep was used according to the manufacturer’s instructions for on column RNA purification. Residual chromosomal DNA was removed by 30 min off column treatment of the samples with TURBO DNA-free Kit. The resulting mRNA was subsequently cleaned with RNeasy Mini Kit. The RNA quantity and quality were checked by UV spectroscopy and RNA 6000 Nanochip.
Label cy3
Label protocol Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)
 
 
Hybridization protocol Hybridization was performed as described in van Melis et al., 2011
Scan protocol Slides were scanned with Agilent G2505C scanner
Description Expression ratio of L1_50B and L1_90A
Data processing Microarrays were normalized using the approach reported previously (by van Melis et al 2011) for germinating spores involving the creation of so called synthetic microarrays. The background-corrected, raw signals (Cy3 and Cy5 channel) of all arrays were hierarchically clustered (Pearson correlation, complete linkage) using Genemaths XT. New synthetic arrays were defined from sample pairs showing the highest similarity in the clustering. The synthetic microarrays were Lowess normalized and all pairwise ratios were determined. The Lowess-normalized data are available on the series record in the file: cybert_ratios.xlsx. The sample data table contains the normalized Cy5/Cy3 values that were used in the first step of the analysis.
 
Submission date Sep 15, 2015
Last update date Feb 02, 2016
Contact name Jos Boekhorst
E-mail(s) [email protected]
Organization name NIZO food research
Street address Kernhemseweg 2
City Ede
ZIP/Postal code 6718 ZB
Country Netherlands
 
Platform ID GPL19768
Series (1)
GSE73043 Identification of CdnL, a putative transcriptional regulator involved in repair and outgrowth of heat-damaged Bacillus cereus spores

Data table header descriptions
ID_REF
VALUE Normalized ratio (Cy5/Cy3)

Data table
ID_REF VALUE
BC0001 1.151532
BC0002 1.29062
BC0003 1.076489
BC0004 0.932765
BC0005 1.007833
BC0006 0.656431
BC0012 1.921992
BC0013 1.163551
BC0014 0.602509
BC0015 0.700231
BC0016 0.89727
BC0017 1.02712
BC0019 0.760473
BC0020 0.968431
BC0021 1.085344
BC0022 1.609577
BC0023 1.197654
BC0024 1.028055
BC0025 0.902936
BC0026 0.961449

Total number of rows: 5270

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM1881351_US22502548_251734310065_S01_GE2_107_Sep09_2_2.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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