SRX971847 GSM1646274 SRP056660 SRS886869 GSM1646274 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646274 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646274 gds 301646274 GEO Accession GSM1646274 SRX971848 GSM1646275 SRP056660 SRS886868 GSM1646275 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646275 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646275 gds 301646275 GEO Accession GSM1646275 SRX971849 GSM1646276 SRP056660 SRS886867 GSM1646276 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646276 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646276 gds 301646276 GEO Accession GSM1646276 SRX971850 GSM1646277 SRP056660 SRS886866 GSM1646277 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646277 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646277 gds 301646277 GEO Accession GSM1646277 SRX971851 GSM1646278 SRP056660 SRS886865 GSM1646278 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646278 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646278 gds 301646278 GEO Accession GSM1646278 SRX971852 GSM1646279 SRP056660 SRS886864 GSM1646279 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646279 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646279 gds 301646279 GEO Accession GSM1646279 SRX971853 GSM1646280 SRP056660 SRS886863 GSM1646280 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646280 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646280 gds 301646280 GEO Accession GSM1646280 SRX971854 GSM1646281 SRP056660 SRS886862 GSM1646281 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646281 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646281 gds 301646281 GEO Accession GSM1646281 SRX971855 GSM1646282 SRP056660 SRS886861 GSM1646282 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit. One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments. Illumina Genome Analyzer IIx GEO Sample GSM1646282 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1646282 gds 301646282 GEO Accession GSM1646282