Array-CGH profiles from 159 neuroblastoma tumors were generated using 44 K or 105 K oligonucleotide microarrays as described previously [23 (link), 24 (link)]. The raw data were analyzed by Agilent Genomics Workbench software (v. 7.0; Agilent Technologies, Santa Clara, CA, USA, 2012) [23 (link)]. Array-CGH data are available as a subset at Gene Expression Omnibus (Accession: GSE45480).
FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [19 (link), 25 (link)]. Genomic DNA from 47 primary neuroblastoma specimens (high FOXP1 expression, n = 23; low FOXP1 expression, n = 24, as defined by the cutoff value for dichotomization of FOXP1 expression) and the neuroblastoma cell line IMR-32 was used to sequence three selected DNA regions covering 45 CpG units downstream of the FOXP1 start site (Table1 ). PCR Primers were designed by using Methprimer (http://www.urogene.org/methprimer/ , Additional file 1 : Table S1).
FOXP1 promoter methylation analysis was performed by Sequenom Inc. (Hamburg, Germany) as described elsewhere [19 (link), 25 (link)]. Genomic DNA from 47 primary neuroblastoma specimens (high FOXP1 expression, n = 23; low FOXP1 expression, n = 24, as defined by the cutoff value for dichotomization of FOXP1 expression) and the neuroblastoma cell line IMR-32 was used to sequence three selected DNA regions covering 45 CpG units downstream of the FOXP1 start site (Table
| Number of DNA samples | 48 |
| Number of genomic regions | 1 |
| Number of amplicons | 3 |
| Number of CpG units | 45 |
| Median amplicon length | 413 bp (min = 365; max = 435) |
| Median CpG/amplicon | 14 CpG/amplicon (min = 11; max = 20) |