The relative quantitative value of each targeting gene was analyzed by using a comparative copy number.
Based on "Comparative copy number variation from whole genome sequencing", by Angel Janevski, Vinay Varadan, Sitharthan Kamalakaran, Nilanjana Banerjee and Nevenka Dimitrova which appeared in Genomic Signal Processing and Statistics (GENSIPS), 2011 IEEE International Workshop on.
The first, array comparative genomic hybridization (aCGH), reports relative copy number to a reference (C57BL/6 J) [ 3– 10].
For quantification of gene relative copy number, we used the comparative Ct method [33].
Relative copy number was calculated using the comparative Ct method, taking PCR efficiency into account.
Levels of BORIS mRNA were expressed in relative copy numbers normalised against the housekeeping gene GAPDH (comparative CT method).
The relative copy number of gene mRNAs was calculated according to the 2-∆∆CT comparative CT method [ 84].
Comparative analysis of copy number alterations in chromosomally unstable murine T-cell lymphomas and human solid tumours identified recurrent aberrations in the mouse that are conserved in human T-ALL but also in other human tumour types [287].
The representation and dynamics of the ten copia-type families were further revealed by comparative analysis of copy number and presence of genes in their flanking sequences in the jatropha genome, and finally copia-type families Jc1, 2, 3, 7, and 9 were found as noteworthy candidates for the development of DNA marker systems in jatropha.
CNV: Copy number variants; aCGH: Array comparative genomic hybridization; CNVR: Copy number variants region; PCA: Principal component analysis; AU: Approximate unbiased; BP: bootstrap probability; qPCR: quantitative polymerase chain reaction; EDN3: Endothelin 3; QC: Quality control; GEO: Gene expression omnibus The authors have declared that no competing interests exist.
ADM-2: Aberration detection method 2; Array CGH: array comparative genomic hybridization; CNA: copy number alterations; CNV: copy number variations; 1 M array: array CGH containing one million (1 × 1 M) oligonucleotide probes; 244 K array: array CGH containing 244 000 oligonucleotide probes; WGA: whole genome amplification.
