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Sample GSM1064950 Query DataSets for GSM1064950
Status Public on Dec 21, 2015
Title Bacteria_acid_rep3
Sample type RNA
 
Source name bacterial cells, acidic shock
Organism Mesorhizobium japonicum MAFF 303099
Characteristics treatment: acidic shock
Treatment protocol Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control. For acidic shock experiments, cells grown overnight at 28 ºC were subjected to an acidic shock of pH 3 at 28 ºC for 30 min.
Growth protocol 10 ml of cells with an OD(540 nm)=0.3, which corresponds to approximately 6x10exp8 cells per ml were used.
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (Qiagen) manufacturer's protocol
mRNA enrichment protocol: MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) - Manufacturer's protocol
Label Cy3
Label protocol aRNA amplification protocol: MessageAmp™ II-Bacteria Kit (Ambion) - Manufacturer's protocol
Quick Amp Labeling Kit (Agilent) - Manufacturer's protocol
 
Hybridization protocol One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol
Scan protocol One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol
Data processing The signal intensity for each spot was extracted using QuantArray Analysis Software (GSI Lumonics). Analysis of raw data was performed using BRB-ArrayTools v3.4.0, where each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. The normalized dataset was then subjected to statistical analysis and clustering using MeV software to identified the diferencially expressed genes. The same dataset was also used to calculate the M-value and Fold-change variation.
 
Submission date Jan 16, 2013
Last update date Dec 21, 2015
Contact name Marta Laranjo
E-mail(s) [email protected]
Organization name Universidade de Evora
Department ICAAM
Street address Apartado 94
City Evora
ZIP/Postal code 7002-554 Evora
Country Portugal
 
Platform ID GPL16511
Series (1)
GSE43527 Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an acidic shock

Data table header descriptions
ID_REF
VALUE Signal intensity, normalized by the median, using the BRB Addin for Excel

Data table
ID_REF VALUE
7204945 11.24511909
7204948 9.602571487
7204950 9.579586983
7204953 11.65537071
7204956 9.910300255
7204958 11.30076313
7204961 10.31457424
7204962 9.699819565
7204965 11.24605179
7204968 9.689620972
7204971 10.00204372
7204973 10.04395008
7204975 10.00420761
7204979 10.50622559
7204980 9.981384277
7204982 9.687410355
7204983 9.920829773
7204986 11.52831459
7204988 12.05409145
7204992 13.46705818

Total number of rows: 7289

Table truncated, full table size 141 Kbytes.




Supplementary file Size Download File type/resource
GSM1064950_7_acid.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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