RNA-seq transcriptomics of the Atp7b-/- mouse liver at six weeks of age

We report liver transcript profiling by RNA sequencing of Atp7b-/- and wild type mice at six weeks of age. Transcriptional network analysis of RNA-seq data reveals a highly interconnected network of transcriptional activators with over-representation of zinc-dependent and zinc-responsive transcription factors. Overall design: Wild type and Atp7b-/- Mice were maintained on strain C57BL x 129S6/SvEv. Housing was in shoebox cages and fed Mazuri Rodent diet (PMI Nutrition, Inc., Richmond, Indiana), containing 16 ppm Cu, 100 ppm Zn, and 235 ppm Fe and water ad libitum, with a 12-hour light/dark cycle. Six-week-old mice of both sexes were used for transcriptomic studies. Animals were sacrificed by carbon dioxide asphyxiation and liver tissue was harvested for RNA isolation. RNA sequencing was performed at the National Center for Genome Resources (NCGR) using the GAIIx platform. Average read quality was 38. An initial dataset was generated using two wild type and two Atp7b-/- samples with singleton 1x54 runs with 15,823,058; 8,149,631; 22,931,967 and 9,538,147 reads. A second paired end (2x54) dataset was generated to augment the initial singleton dataset with one wild type and one Atp7b-/- run resulting in 36,360,686 and 38,366,743 reads, respectively.

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Meacham KA, Cortés MP, Wiggins EM, Maass A, Latorre M, Ralle M, Burkhead JL