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Sample GSM1652910 Query DataSets for GSM1652910
Status Public on Apr 15, 2016
Title T24_rep3_planc
Sample type RNA
 
Source name Planktonic cell 24 hours
Organism Rhizobium etli CFN 42
Characteristics cell type: Planktonic cells
Treatment protocol Separated after 24 hours and 72 hours by centrifugation (13,000g 10 min) using 150 mL culture and mixed with RNA later AMBION (RNA stabilization solution).
Growth protocol The bacteria cultures were incubated at 29ÂșC 60% of relative humidity and sessile and planktonic cells were cultured both in the same bootle and separed after 24 and 72 hours by centrifugation.
Extracted molecule total RNA
Extraction protocol We used 100 ml cultures samples (planktonic and sessile). Total RNA was isolated by acid hot phenol extraction as described previously by De Vries et al., (1993).
Label Cy3
Label protocol The RNA was differentially labeled with Cy3-dCTP and Cy5-dCTP using a CyScribe first-strand cDNA labeling Kitt (Amersham Biosciences).
 
Hybridization protocol Pairs of Cy3- and Cy5-labeled cDNA samples were mixed and hybridized with the array as described by Hedge et al. (2000).
Scan protocol After the arrays were washed, they were scanned using a pixel size of 10 mm with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA).
Data processing Spot detection, determination of mean signals and mean local background intensities, image segmentation, and signal quantification were performed for the microarray images using the Array-Pro Analyzer 4.0 software (Media Cybernetics, L.P.).
The analysis consisted of three steps: background subtraction and data normalization, analysis of variance, and controlling for the expected number of false positives (Quackenbush 2002). The raw data microarray data were normalized to have comparable signal values between the different microarray slides. After background subtraction, data were quantile-normalized using the q-spline method (Workman et al. 2002), attaining signal intensities with the same distributions between all microarray slides in the red and green channels. The signals were transformed to logarithmic scale (log2), and the resulting signals were examined using M-A plots
To determine the significance of the expression differences from planktonic and sessile samples, data were subjected to ANOVA analysis, and a p-value <0.01 was considered as significant. Thus an expected 10% of false positives were accepted. Microarray data were analyzed to assess the statistical significance of expression differences between planktonic and sessile organisms after 24 and 72 hours biofilm maturation stages. The analysis consisted of three steps: background subtraction and data normalization, analysis of variance, and controlling for the expected number of false positives (Quackenbush, 2002).
 
Submission date Apr 08, 2015
Last update date Apr 15, 2016
Contact name AGUSTIN REYES PEREZ
E-mail(s) [email protected]
Phone +527773291899
Organization name UNAM
Department FUNCTIONAL GENOMICS
Lab PROTEOMICS
Street address UNIVERSITY AV.
City CUERNAVACA
State/province MORELOS
ZIP/Postal code 62210
Country Mexico
 
Platform ID GPL10081
Series (1)
GSE67656 A landscape of cellular aggregation of Rhizobium etli CFN42 by a transcriptomic approach

Data table header descriptions
ID_REF
VALUE Normalized signal

Data table
ID_REF VALUE
1 21290.27111
2 3121.997646
3 10492.46286
4 10097.74397
5 10581.87655
6 6721.336437
7 16216.86393
8 15188.3176
9 6262.372118
10 5239.231451
11 6128.098095
12 4504.26831
13 6065.244371
14 6750.770595
15 9537.755783
16 6959.404694
17 17844.04829
18 10537.33071
19 8862.615324
20 4781.74547

Total number of rows: 12672

Table truncated, full table size 206 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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