Mitochondrial Genome Analysis Using MitoChip v2.0

Analysis of mtDNA sequence variations was done using GeneChip™ Human Mitochondrial Resequencing Arrays 2.0 (MitoChip v2.0) [44 (link)]. For processing of the arrays, the GeneChip® CustomSeq® Resquencing Array Protocol version 2.1 was used with the following modification: instead of using long-range PCR, mtDNA was amplified using the REPLI-g mitochondrial DNA kit (Qiagen Hilden, Germany), as it has been described for MitoChip experiments before [45 (link)], and purified using Agencourt® AMPure® XP magnetic beads (Qiagen Supplementary Protocol, REPLI-g mitochondrial DNA kit). After purification, 270 ng of mtDNA was fragmented and labeled using the GeneChip® Resequencing Assay Kit (Affymetrix, now part of ThermoFisher Scientific). After hybridization, MitoChip v2.0 arrays were washed and stained in a Fluidics Station 450 before being scanned in Affymetrix GeneChip Scanner 3000 7G. CEL files were acquired by GeneChip® Operating Software 1.4 (GCOS 1.4.0.036) and analyzed with GeneChip® Sequence Analysis Software (GSEQ 4.1). Complete microarray data are available at Gene Expression Omnibus (GEO accession number: GSE211250).

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Brockmann S.J., Buck E., Casoli T., Meirelles J.L., Ruf W.P., Fabbietti P., Holzmann K., Weishaupt J.H., Ludolph A.C., Conti F, & Danzer K.M. (2023). Mitochondrial genome study in blood of maternally inherited ALS cases. Human Genomics, 17, 70.

Publication 2023

REPLI-g mitochondrial DNA kit AMPure® XP magnetic beads GeneChip® Resequencing Assay Kit GeneChip Scanner 3000 7G

Assay Gene expression Genechip Human Hybridization Microarray Mitochondrial Mtdna Sequence analysis Sequence variations

Corresponding Organization :

Other organizations : Universität Ulm, German Center for Neurodegenerative Diseases, Istituto Nazionale di Riposo e Cura per Anziani, Istituti di Ricovero e Cura a Carattere Scientifico

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Variable analysis

independent variables

MtDNA amplification method (REPLI-g mitochondrial DNA kit)

dependent variables

MtDNA sequence variations

control variables

GeneChip® CustomSeq® Resquencing Array Protocol version 2.1

controls

Positive control: None specified
Negative control: None specified

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