Meta-data for the data set associated with the publication Ian Dworkin, Julie Brown Anderson, Youssef Idaghdour, Erin Kennerly Parker, Eric Stone, and Greg Gibson. 2011.The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc, and its association with wing shape in Drosophila melanogaster.GENETICS/2010/125922 (In Press) This data was provided by (and for questions please contact): Ian Dworkin Department of Zoology 203 Natural Sciences Bldg. Michigan State University East Lansing, MI idworkin "AT" msu dot edu # The associated data includes both the microarray data used for this study, as well as the wing shape phenotypes (line means for the partial warps and uniform components describing variation for wing shape). For the file: alleles_for_P_arrays.csv # These just describe the different genotypes used in this study Line = line number based on Bloomington Stock number allele = allele name (including gene) gene = gene name For the file: partial_warps_wings_For_PLS.csv # This has the "line means" for the partial warps (X1-X6,Y1-Y6) and uniform components (UniX, UniY) for the wing shape data used for the PLS analysis with gene expression. Column names: allele = allele name gene = gene of mutant, or name of wild-type strain (Sam & Ore) Line = Bloomington Stock Number Genotype = mutant ( p ) or wild type (w) Sex = All male (M) for this analysis X1 X2 X3 X4 X5 X6 Y1 Y2 Y3 Y4 Y5 Y6 UniX UniY For the file: P_element_probe_labels_illumina.csv # This has all of the generic information for the Microarray # Also see NCBI GEO GPL7740 for more information on this platform TargetID = Illumina identifier SYMBOL = gene name DEFINITION = information on the gene GID = gene identifier ProbeID = unique probe identifier START = start position of the probe PROBE_SEQUENCE = sequence of the probe For the file: P_element_arrays_vetted.csv # This contains the raw gene expression data used in the study for all of the P-element insertion mutants. ProbeID = Name of the probe used (see file P_element_probe_labels_illumina.csv or NCBI GEO GPL7740). Label = Unique Slide (left hand side of dash) and array (RHS of dash) identifier Raw_Expression = Raw expression LINE = Bloomington Stock number (see alleles_for_P_arrays.csv) REP = Biological Replicate of sample labeling = labeling replicate Sample_Group = identifier of line_rep_labeling Sentrix_Position = Position of array within slide hyb_date = date of hybridization array = my own identifier for the slide (16 arrays/slide) array_dummy = my own unique identifier for the array For the file: sd_illumina.csv # This was a smaller seperate experiment to test the general efficacy of the Illumina array platform. Here we repeated the experiment from: Dworkin I, Kennerly E, Tack D, Hutchinson J, Brown J, Mahaffey J, Gibson G. 2009. Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila melanogaster. Genetics 181(3):1065-76. PMID: 19064709 doi:10.1534/genetics.108.096453 also see NCBI GEO GSE13779 for the raw data from the 2009 paper. Column headers: Array = Unique identifier for array on the slide (only 1 slide, with 16 arrays/slide) Background = wild-type genetic background (Ore=Oregon-R, Sam=Samarkand) Genotype = Genotype (wt=wild-type, sd = scalloped[E3]) biol_rep = biological replicate label_rep = labeling replicate TargetID = Illumina identifier ProbeID = # probe used (see file P_element_probe_labels_illumina.csv or NCBI GEO GPL7740). SYMBOL = gene symbol (corresponding to the probe) DEFINITION = information on the gene GID = gene identifier expression = raw expression log2_exp = log2(raw expression)