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To determine which growth factors contribute to enhanced hematopoietic regeneration after autologous HSCT, we used Human Cytokine Antibody Arrays for analysis of 174 chemokines (figure S2).
The microarray-based study of global gene responses was performed in triplicate for each time point, yielding 27 arrays for analysis.
Each array included in the final analysis had at least 30% of the probesets detected above background (percent present >30%) and a 3' to 5' ratio of signal intensity for GAPDH of less than or equal to 5. One never smoker microarray was excluded based on these quality control filters (low percent present, high 3' to 5' GAPDH ratio), leaving four never and four current smoker arrays for analysis.
Results were collected into tab delimited text files for each of the four experimental arrays for analysis with Agilent Technologies software GeneSpring GX (v10.0.1).
However, our data for the kingbird (Fig. 3) suggest that use of zebra finch arrays for analysis of sub-oscines (divergence time ~70 MYA) may be more problematic.
Three independent biological replicates of the control culture and ranalexin treatment were performed and the RNA derived from these was labelled and co-hybridised as two dye-swapped technical replicates, providing a total of six arrays for analysis.
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We developed a 60mer oligo-array for analysis of gene expression from each locus.
Maize is one of the most important crop plants worldwide, however a high density SNP genotyping array for analysis of its large and highly dynamic genome was not available so far.
cDNA arrays allowed for analysis of the four distinct groups as they require smaller amounts of sample material.
All the arrays used for analysis have been fabricated in house from a unique set of PCR products and these have been validated in numerous studies [ 7- 15].
Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays.
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