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Sample GSM1064960 Query DataSets for GSM1064960
Status Public on Dec 31, 2016
Title Bacteria_salt_rep3
Sample type RNA
 
Source name bacterial cells, salt shock
Organism Mesorhizobium japonicum MAFF 303099
Characteristics treatment: salt shock
Treatment protocol Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control.For salt shock experiments, cells grown overnight at 28 ºC were subjected to a salt shock of 10% NaCl 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 31, 2016
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)
GSE43530 Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an salt 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 10.06092548
7204948 10.31915283
7204950 10.38665676
7204953 12.5974741
7204956 9.310839653
7204958 11.78927994
7204961 11.72540188
7204962 11.40834904
7204965 11.66031837
7204968 9.955325127
7204971 9.689764977
7204973 10.2510128
7204975 9.815073967
7204979 9.824979782
7204980 11.04614639
7204982 9.693387985
7204983 9.620934486
7204986 9.660987854
7204988 12.76644802
7204992 13.61571693

Total number of rows: 7289

Table truncated, full table size 141 Kbytes.




Supplementary file Size Download File type/resource
GSM1064960_7_salt.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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