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Blood, Vol. 106, Issue 9, 3214-3222, November 1, 2005
Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes
Blood Rubio-Moscardo et al.
106: 3214
Supplemental materials for: Rubio-Moscardo et al, Vol 106, Issue 9, 3214-3222
Full sequencing of the common region of deletion in the Z138 cell lines: This cell line had the shortest interval of loss in 8p21. Primers were designed to amplify the DNA sequence of the ∼1 Mb segment between BACs RP11-177H3 and RP11-677P13. To screen for any possible mutation, sequences were compared to the corresponding UCSC database.
Files in this Data Supplement:
- Table S1. Experimental procedures (XLS file, 45 KB)
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Primers used for mRNA amplification in RT-PCR analyses. QRT-PCR reactions were performed using the ABIPrism 7700 (PE Applied Biosystems) and the SYBR Green I dye. mRNA expression of TRAIL-R1 and TRAIL-R2 was normalized to RNA content for each sample by using GADPH and TBP gene products as internal controls. The relative expression was calculated as the ratio of the expression from each tumor compared with the average expression from the blood mononuclear cells obtained from 12 healthy donors. Mutation analysis of TRAIL receptor genes: thirty-five sets of primers were designed to amplify exons plus flanking intron sequence for TRAIL-R1, TRAIL-R2, TRAIL-R3, and TRAIL-R4, using the Primer 3 program (http://www-genome.wi.mit.edu). The PCR amplification products were purified using a QIAquick PCR Purification Kit (Qiagen) and both DNA strands sequenced by cycle sequencing. Sequence variations were compared with published sequences. Methylation analysis: sequence primers were designed in 5′ untranslated region CpG islands of the published sequences near translation start sites.
- Table S2. Mutation analyses of TRAIL-receptor, PPP3CC, and DBC2 genes (XLS file, 49 KB)
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Description of polymorphisms corresponding to TRAIL receptor, PPP3CC, and DBC2 genes in cell lines and patient biopsies.
- Table S3. Supplementary data from array CGH (B1) and lymphochip microarray (B2), including 8p BAC and cDNA clone content and individual genomic and gene expression measurements (XLS file, 120 KB)
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