Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray

Table 2 Summary of CIZ1 alternative splicing in SKNMC cell line

SKNMC exon probes	Average of 3 technical replicates (B1)	Biological replicate 2	Biological replicate 3
Ciz1-ex1b2	+	=	=
Ciz1-intron 12	-	=	-
SKNMC junction probes
Ciz1-ex8a0-ex12a1	+	+	+
Ciz1-ex8af2-ex15	+	+	=
Ciz1-ex12-ex13	+	+	+
Ciz1-ex15-ex16	-	=	=

Three independent RNA isolates from proliferating SKNMC cell (Biological replicates, B1, B2 and B3) were analysed on individual arrays, with one isolate undergoing analysis in triplicate (technical replicate, T1, T2 and T3 shown in Fig. 2A and 3). Probes that are up or down regulated more that 1.5 fold and who's SEM indicate agreement between three technical replicates are shown. Results for these probes derived from the two further biological replicates (replicate 2 and replicate 3) are also shown. + indicates significantly up-regulated, - indicates significantly down-regulated and = indicates no significant change. Significance is taken to be a change that is ≥ 1.5 fold compared to control RNA. For paediatric cancer cell line SKNMC, expression of two probes was consistently and significantly altered compared to control samples, these are Ciz1-ex8a0-ex12a1 and Ciz1-ex12-ex13. Raw data is given in Additional file 5, tables S4-S8.

ISSN: 1471-2407