Transcriptomics

Dataset Information

6

SSHscreen analysis of cowpea drought stress SSH libraries (F&R) to calculate Enrichment ratio 2 and 3 values


ABSTRACT: Screening cDNA clones from SSH library by hybridization with cDNA used to construct the library. Treated samples were drought-stressed cowpea plants, and control samples were cowpea plants subjected to a standard watering regime. cDNA clones from forward and reverse libraries are spotted on the same array, but data from each library were analysed separately after normalization using SSHscreen software (http://microarray.up.ac.za/SSHscreen ) to calculate Enrichment Ratio 3 (ER3) and Enrichment Ratio 2 (ER2) values for each clone. ER3 is a measure of differential expression, and was determined using a set of hybridizations with unsubtracted treated (UT) and unsubtracted control (UC) cDNA. ER2 is a measure of the relative abundance of a clone's transcript in the original tester sample, relative to other transcripts in the sample prior to the SSH process. ER2 for the forward library was determined using a set of hybridizations with subtracted treated (ST) and unsubtracted treated (UT) cDNA. ER2 for the reverse library is determined using a set of hybridizations with subtracted control (SC) and unsubtracted control (UC) cDNA. Direct comparison of UT and UC cDNAs to calculate ER3 values for F and R library, including dye swaps and replicate arrays. Direct comparison of ST and UT cDNAs to calculate ER2 values for F library, including dye swaps and replicate arrays. Direct comparison of SC and UC cDNAs to calculate ER2 values for R library, including dye swaps and replicate arrays.

ORGANISM(S): Vigna unguiculata  

SUBMITTER: Nanette Coetzer  Inge Gazendam  Dave K Berger 

PROVIDER: E-GEOD-20273 | ArrayExpress | 2010-05-05

SECONDARY ACCESSION(S): GSE20273PRJNA125255

REPOSITORIES: GEO, ArrayExpress

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