SRX700834 GSM1504011 SRP047122 SRS700952 GSM1504011 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504011 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504011 gds 301504011 GEO Accession GSM1504011 SRX700835 GSM1504002 SRP047122 SRS700953 GSM1504002 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504002 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504002 gds 301504002 GEO Accession GSM1504002 SRX700836 GSM1504003 SRP047122 SRS700954 GSM1504003 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504003 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504003 gds 301504003 GEO Accession GSM1504003 SRX700837 GSM1504004 SRP047122 SRS700955 GSM1504004 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504004 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504004 gds 301504004 GEO Accession GSM1504004 SRX700838 GSM1504005 SRP047122 SRS700956 GSM1504005 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504005 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504005 gds 301504005 GEO Accession GSM1504005 SRX700839 GSM1504006 SRP047122 SRS700957 GSM1504006 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504006 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504006 gds 301504006 GEO Accession GSM1504006 SRX700840 GSM1504007 SRP047122 SRS700958 GSM1504007 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504007 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504007 gds 301504007 GEO Accession GSM1504007 SRX700841 GSM1504008 SRP047122 SRS700960 GSM1504008 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504008 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504008 gds 301504008 GEO Accession GSM1504008 SRX700842 GSM1504009 SRP047122 SRS700959 GSM1504009 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504009 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504009 gds 301504009 GEO Accession GSM1504009 SRX700843 GSM1504010 SRP047122 SRS700961 GSM1504010 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504010 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504010 gds 301504010 GEO Accession GSM1504010 SRX700844 GSM1504012 SRP047122 SRS700962 GSM1504012 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504012 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504012 gds 301504012 GEO Accession GSM1504012 SRX700845 GSM1504013 SRP047122 SRS700963 GSM1504013 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504013 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504013 gds 301504013 GEO Accession GSM1504013 SRX700846 GSM1504014 SRP047122 SRS700964 GSM1504014 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504014 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504014 gds 301504014 GEO Accession GSM1504014 SRX700847 GSM1504015 SRP047122 SRS700965 GSM1504015 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504015 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504015 gds 301504015 GEO Accession GSM1504015 SRX700848 GSM1504016 SRP047122 SRS700966 GSM1504016 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504016 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504016 gds 301504016 GEO Accession GSM1504016 SRX700849 GSM1504017 SRP047122 SRS700967 GSM1504017 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504017 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504017 gds 301504017 GEO Accession GSM1504017 SRX700850 GSM1504018 SRP047122 SRS700968 GSM1504018 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504018 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504018 gds 301504018 GEO Accession GSM1504018 SRX700851 GSM1504019 SRP047122 SRS700969 GSM1504019 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504019 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504019 gds 301504019 GEO Accession GSM1504019 SRX700852 GSM1504020 SRP047122 SRS700970 GSM1504020 RNA-Seq TRANSCRIPTOMIC cDNA Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled. The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany). Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123). Illumina Genome Analyzer II GEO Sample GSM1504020 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1504020 gds 301504020 GEO Accession GSM1504020