SRX028135 RC-seq SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS115358 Hippocampus SA RC-seq post-hybridisation Hippocampus SA OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina Genome Analyzer II SRX028156 RC-seq Caudate1 SA SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS115354 Caudate1 SA RC-seq post-hybridisation Caudate1 SA OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina Genome Analyzer II SRX028157 RC-seq Caudate2 SA SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS115355 Caudate2 SA RC-seq post-hybridisation Caudate2 SA OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina Genome Analyzer II SRX028158 RC-seq Hippocampus SB SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS115356 Hippocampus SB RC-seq post-hybridisation Hippocampus SC OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 101 Illumina Genome Analyzer II SRX028159 RC-seq Caudate SB SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS115357 Caudate SB RC-seq post-hybridisation Caudate SC OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 101 Illumina Genome Analyzer II SRX043526 Pooled blood SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS172932 Pooled blood RC-seq post-hybridisation pooled blood OTHER GENOMIC other 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina Genome Analyzer II SRX063321 RC-seq Hippocampus person 2 SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS193270 Hippocampus person 2 RC-seq post-hybridisation Hippocampus subject B OTHER GENOMIC Hybrid Selection 302 0 Application Read Forward 1 1 Application Read Reverse 152 Illumina Genome Analyzer II SRX063322 RC-seq Caudate nucleus person 2 SRP003677 RC-seq Libraries were processed prior to array hybridization by adding the following components to a 1.5ml tube: 320ng of library material, 0.64µl of 100µM Illumina primer PE 1.0 and PE 2.0 and 64µl of Roche NimbleGen proprietary capture enhancing (PCE) compound (in place of Cot-1 repetitive DNA blocker). Samples were dried down by puncturing a hole in the 1.5ml tube cap with a 20 gauge needle and processing in an Eppendorf Vacufuge (San Diego, CA) set to 60°C for 20 minutes. Samples were then re-suspended by adding 15.4µl of water and placing tubes on a heating block at 70°C for 10 minutes, followed by vigorous vortex mixing for 30 seconds and centrifugation to recollect any dispersed sample. To each sample tube 25.6µl NimbleGen SC Hybridization Buffer (Part# 05340721001) and 10.24µl NimbleGen Hybridization component A (Part# 05340721001) were added, followed by vortexing for 30 seconds, centrifugation and placement on a heating block at 95°C for 10 minutes. Samples were again mixed for 10 seconds, spun down, and placed in a Roche NimbleGen Hybridization System at 42°C until ready for hybridization. The capture array was comprised of three identical sub arrays of 720K features targeting human retrotransposons (see above). To each slide, a NimbleGen HX3 mixer was affixed according to the manufacturer’s instructions and 16µl of the hybridization mixture (sample library, PCE, Ilumina primers, SC Hybridization Buffer and SC Component A) was pipetted into each of the three sub-array fields. Loading and vent holes were covered with port seals and each sample was hybridized for 72 hours at 42°C on Hybridization Station setting “B”. Slide washing and sample library elution were performed as previously described (Y. Fu et al., Plant J 62, 898). SRS193271 Caudate nucleus person 2 RC-seq post-hybridisation Caudate nucleus subject B OTHER GENOMIC Hybrid Selection 302 0 Application Read Forward 1 1 Application Read Reverse 152 Illumina Genome Analyzer II