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Sample GSM989272 Query DataSets for GSM989272
Status Public on Oct 01, 2012
Title UCD 153 18h 2
Sample type RNA
 
Source name UCD 153 18h 2
Organism Nostoc punctiforme PCC 73102
Characteristics genotype/variation: wild type
Treatment protocol For nitrogen step-down culutres supplemented with 2.5 mM NH4Cl at a chlorophyl a concentration of 2-3 ug/ml were harvested at 1000xg for 5 min, washed 3x with AA/4 and resuspended in AA/4.
Growth protocol Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 30mM fructose.
Extracted molecule total RNA
Extraction protocol RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256).
Label Cy3
Label protocol Ten micrograms of total RNA were used for cDNA synthesis using SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen). 0.5 ug of cDNA was labled with Cy3 dye using the Nimblegen One-color DNA labeling kit.
 
Hybridization protocol Two micrograms of labled cDNA were prepared for hybridization using the Nimblegen hybridization kit and sample tracking controls and hybridized to a Nimblegen 12x135k slide fitted with an HX12 mixer at 42C on a Nimblegen Hybridization System 4 hybridizer for 16-20h.
Scan protocol Following hybridization slides were washed with Nimblegen wash buffer and scanned using a GenePix 4000B scanner using GenePix Pro-6.0 software (Molecular Devices).
Data processing Scanned images (.tif) were imported into NimbleScan software (NimbleGen) where the image containing all 12 arrays on each slide was separated into 12 individual image files. An automatic alignment was performed for each individual array and X, Y, and Signal files (.xys) were generated. Normalization of .xys files was performed using the R package oligo (Carvalho et al, 2007. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8:485-489) and the R package oneChannelGUI (Sanges et al, 2007. oneChannelGUI: A graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinformatics 23:2406-3408) was used to compute a linear model fit and contrasts to generate top tables containing the change in expression between experimental and reference data points as M-values (Log2[experimental]-log2[reference]) along with statistical information such as p-, adjusted p- and B-values. All data and statistical analyses were computed from three independent biological replicates. Contrasts were computed for the patN-deletion strain using the wild-type strain as a reference at each time point (i.e. the ∆patN strain t = 3 h - wild type t = 3 h) (∆patN -wild type contrast) as well as for each time point using t = 0 of the same strain as a reference (i.e. the ∆patN strain t = 3 h – the ∆patN strain t = 0h) (∆patN or wild type time course contrast). Differential expression of genes with B-values > 0 was considered statistically significant. Heat maps were generated using Genesis (Sturn et al, 2002. Genesis: Cluster analysis of microarray data. Bioinformatics 18:207-208) with the M-values from top tables for each time point.
 
Submission date Aug 21, 2012
Last update date Oct 01, 2012
Contact name Douglas D Risser
E-mail(s) [email protected]
Organization name UC Davis
Department Microbiology
Lab Meeks
Street address One Shields Ave
City Davis
State/province California
ZIP/Postal code 95616
Country USA
 
Platform ID GPL15966
Series (1)
GSE40250 Comparative transcriptomics of wild-type (UCD 153) and patN-deletion strains (UCD 524) of Nostoc punctiforme ATCC 29133

Data table header descriptions
ID_REF
VALUE RMA-normalized average gene value intensities

Data table
ID_REF VALUE
NpF0001 6.469265396
NpF0002 5.337318277
NpF0005 9.376244312
NpF0008 8.709025995
NpF0013 12.75231114
NpF0014 5.568278383
NpF0015 8.059381346
NpF0017 7.754488275
NpF0018 7.552055717
NpF0019 6.806220996
NpF0020 13.33623272
NpF0021 10.26966258
NpF0022 9.305693131
NpF0024 5.125089444
NpF0025 12.58304306
NpF0026 9.913010825
NpF0027 6.67223288
NpF0028 11.69067709
NpF0036 6.102751562
NpF0037 6.278357642

Total number of rows: 7151

Table truncated, full table size 139 Kbytes.




Supplementary file Size Download File type/resource
GSM989272_399067A03.xys.gz 710.3 Kb (ftp)(http) XYS
Processed data included within Sample table

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