Striatum, cortex, and liver were selected for full profiling. Specifically, at each of 3 time points (2, 6, 10 months), four female and four male heterozygous KI mice from each of the 6 Htt CAG repeat lengths were profiled, resulting in 48 samples from each tissue and each time point. Additional samples from wild type littermates from the Q20 line were profiled as well (striatum at all 3 ages, cortex and liver at 2 and 10m only). In addition to the fully profiled tissues, 11 other tissues were selected for a smaller study (referred to as the Tissue Survey) involving 8 (4 male and 4 female) wild type mice from the 6-month Q=20 line, and 8 (4 male and 4 female) heterozygous mice from the 6-month Q175 line, for a total of 16 samples per tissue. The 11 tissues include 5 brain regions (brainstem, cerebellum, hippocampus, hypothalamus/thalamus, and corpus callosum) and 6 peripheral tissues (white gonadal adipose, white intestinal adipose, brown adipose, skin, heart, and gastrocnemius muscle). Messenger RNA was extracted and prepared using the Illumina TruSeq RNA sample prep kit and sequenced on an Illumina HiSeq2000 sequencer using strand-specific, paired end, 50-mer sequencing protocols to a minimum read depth of 40 million reads per sample. The sequencing was performed in 2 separate batches (6-month samples in batch 1, 2- and 10-month samples in batch 2). Clipped reads were aligned to mouse genome mm9 using the STAR aligner53 (link) using default settings. Read counts for individual genes were obtained using HTSeq54 (link).