Transcriptional signature of an adult brain tumor in Drosophila

BMC Genomics

Table 1 Overview of the array experiments

		Experiment A	Experiment B
RNA source	brat tumor	adult brat^[k06028]heads	adult brat^[k06028]brains
	control	Oregon RS heads	brat^[k06028] jumpout brains
Arrays used		roDromega full genome	Affymetrix full genome
Number of replicates		5 Oregon RS against 6 brat^[k06028]	6 brat^[k06028] jumpout against 6 brat ^[k06028]
Signal amplification		no	yes
Differentially expressed genes		725	1888
Overlap between the experiments		321

Overview of the two independent genome-wide gene expression studies using two different oligonucleotide array platforms to compare adult control flies with flies displaying the adult brat^k06028mutant brain tumor. Row 1 and Row2 indicate the source from which total RNA was extracted. Row 1 indicates source of tumor tissue, Row 2 indicates source of control tissue used in the experiments. For experiment A (left column), total RNA was isolated from homozygous brat^k06028mutant heads (row 1) as compared to total RNA isolated from Oregon R wildtype heads (row 2). For experiment B (right column), total RNA was isolated from dissected homozygous brat^k06028mutant brains (row 1) as compared to total RNA isolated from dissected brains derived from flies generated by transposon excision of the brat^k06028P-element (termed A2, brat^k06028jumpout; row 2). Row 3 denotes the two different Affymetrix oligonucelotide arrays used. Row 4 indicates the number of replicates carried out per condition for experiment A and experiment B, respectively. Row 5 displays whether or not a signal amplification step has been performed following cRNA hybridization to the arrays. Row 6 presents the number of transcripts differentially expressed between conditions for experiment A and experiment B, respectively. Row 7 indicates the number of genes that passed the filter criteria in both experiments.

ISSN: 1471-2164