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Additional file 3. Genetic deletion of CK2α’ does not ameliorate anxiety-like behaviors or locomotor asymmetry of zQ175 HD at 12 months of age. a-e, Gross motor performance, exploratory behavior, and anxiety-like behavior were assessed during 30 mins in an open field test. a, distance traveled, b, time spent at the center of the field, c, average locomotion velocity and d, time in the outer/inner zone of the field between zQ175 and zQ175:CK2α’ (+/-). e, Representative tracing images show the total distance traveled by the subject. f, Parameters of the spontaneous motor activity (number of rears) evaluated by a cylinder test. Error bars denote mean ± SEM, values were analyzed by two-way ANOVA with Sidak’s post-hoc test. n.s = not significant.

Additional file 6. WGCNA modules genes assignment.

Additional file 15. SNCA regulates the expression of synaptic genes identified in IPA analysis in R6/1 mice. a, IB for α-syn (4D6 antibody) and mtHTT (EM48 antibody) in the striatum of 5 months old WT, SNCAKO, R6/1 and R6/1:SNCAKO (n=3 mice/genotype). b, RT-qPCR analyses for SNCA and genes identified in the IPA analyses to be connected to SNCA; (Ttr, Grm2, Slc17a7, Slc30a3, Cckbr, Nrp2, Tbr1 and Nr4a2) (n = 4-5 mice/genotype). Error bars represent mean ± SEM. Statistical analyses were conducted by Student’s t-test. p-values

Additional file 5. Expressions of all identified co-expression gene modules from WGCNA studies for each mouse sample. A total of 20 different modules were identified when comparing all the genotypes.

Additional file 2. Deficiency in CK2α’ expression does not affect MSN abundance but does influence synaptic genes. a, b, Representative images show the labeling of Ctip2 (a) and quantitative analysis (b) from striatum of zQ175 and zQ175:CK2α’(+/-) mice (n = 3 mice/genotype, at least 3 images averaged/mouse). Scale bar, 50 µm. c, mRNA levels assessed by RT-qPCR of Drd1 and Drd2 (striatal MSN markers), Darpp32 and PSD95 in the striatum of 12 months old mice (n=4 mice/genotype). Error bars denote mean ± SD, values were analyzed by Student’s t-test. p-values

Additional file 7. WGCNA module names and number of genes per module.

Additional file 4. CK2α’ does not alter cognitive behavior in symptomatic HD mice. a, b, Freezing time in the cued (a) and contextual fear conditioning test (b). c-e, Performance on the Barnes maze (BM) task measured by latency to reach the escape hole (c), the mean distance from the target location (d), and total distance until escape in training sessions (e). f-h, Results of BM reversal test are similar to those in BM test, measured by latency to first entry (f), total distance traveled (g) and the mean distance from the target location (h). i, working memory, percent of spontaneous alternation measured by Y maze. Tests were conducted in 12 month old zQ175 and zQ175:CK2α’(+/-).Error bars represent mean ± SEM. Statistical analyses were conducted using ANOVA with Sidak’s post-hoc test (n = 6 mice/genotype). n.s = not significant.

Additional file 8. RNA-Seq comparison between samples and with Langfelder et al., 2016 [49]. a, Kruskal-Wallis test of module expressions between zQ175 mice and WT mice. b IPA canonical pathway analysis of module genes for module “Red”. c, Cook’s distance (DESeq2), which is a measure of how much a single sample is influencing the fitted coefficients for a gene, for all tested samples (HET = CK2α’(+/-), KI = zQ175, KIHET = zQ175:CK2α’(+/-)). d, Network visualization of top 15% connected genes for module genes of module “Greenyellow”. The size of the circles was scaled by the absolute value of the mean log2-fold change between zQ175 and zQ175:CK2α’(+/-) mice. e, MA-plot of differential gene expression between HD (zQ175) and WT mice. f, Venn Diagram of differentially expressed genes between HD (zQ175) and WT mice in comparison to Langfelder 2016 data. g, MA-plot of differential gene expression between zQ175:CK2α’(+/-) and WT mice. h, Venn Diagram of differentially expressed genes between zQ175, WT, zQ175:CK2α’(+/-) and CK2α’(+/-) mice. i, Driver factors of gene expression variance (genotype and/or gender) for the DGEs identified between zQ175 and zQ175:CK2α’(+/-) were evaluated using R package variance Partition.