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Supplementary data
Tumor microenvironment associated modifications of alternative splicing
Quantitative RT-PCR primer validation
ASEs
Test in FFPE pool
Primer Validation Analysis
: RefSeq BSP OSG3 NA primer validation
RefSeq BSP OSG3 NA primer validation
| Gene | Detection | Plate positions | Primers | Realtime | ||||||
| Plate | Row | Col | Forward | Reverse | Curve | NTC | CGE | Conclusion | ||
| ADAM33 | short | CM020797 | 1 | 1 | ADAM33_cass_S_f | ADAM33_cass_S_r | BAD | BAD | BAD | BAD |
| ADAM33 | short | CM020797 | 1 | 2 | ADAM33_cass_S_1_f | ADAM33_cass_S_r | BAD | GOOD | BAD | BAD |
| AGC1 | long | CM020797 | 1 | 3 | AGC1_cass_L_f | AGC1_cass_L_r | BAD | GOOD | BAD | BAD |
| AGC1 | long | CM020797 | 1 | 4 | AGC1_cass_L_1_f | AGC1_cass_L_r | BAD | GOOD | BAD | BAD |
| AKAP7 | long | CM020797 | 1 | 5 | AKAP7_cass_L_f | AKAP7_cass_L_r | BAD | GOOD | BAD | BAD |
| ALOX15B | short | CM020797 | 1 | 6 | ALOX15B_cass_S_f | ALOX15B_cass_S_r | BAD | GOOD | BAD | BAD |
| ANKMY1 | short | CM020797 | 1 | 7 | ANKMY1_cass_S_f | ANKMY1_cass_S_r | BAD | GOOD | BAD | BAD |
| ANKMY1 | short | CM020797 | 1 | 8 | refseq_ANKMY1.F4 | ANKMY1_cass_S_r | BAD | GOOD | BAD | BAD |
| ATP11C | long | CM020797 | 1 | 9 | ATP11C_cass_L_1_f | ATP11C_cass_L_2_r | GOOD | GOOD | GOOD | GOOD |
| BTLA | short | CM020797 | 1 | 10 | BTLA_cass_S_f | BTLA_cass_S_r | BAD | GOOD | BAD | BAD |
| BTLA | short | CM020797 | 1 | 11 | BTLA_cass_S_f | BTLA_cass_S_1_r | BAD | BAD | BAD | BAD |
| BTN2A2 | short | CM020797 | 1 | 12 | BTN2A2_cass_S_2_f | BTN2A2_cass_S_2_r | BAD | BAD | BAD | BAD |
| C14orf138 | long | CM020797 | 2 | 1 | C14orf138_cass_L_1_f | C14orf138_cass_L_r | BAD | GOOD | BAD | BAD |
| C14orf138 | long | CM020797 | 2 | 2 | C14orf138_cass_L_f | C14orf138_cass_L_r | BAD | GOOD | BAD | BAD |
| C14orf138 | short | CM020797 | 2 | 3 | C14orf138_cass_S_f | C14orf138_cass_S_1_r | BAD | GOOD | BAD | BAD |
| CACNA2D4 | short | CM020797 | 2 | 4 | CACNA2D4_cass_S_f | CACNA2D4_cass_S_r | GOOD | GOOD | GOOD | GOOD |
| CCL4 | short | CM020797 | 2 | 5 | CCL4_cass_S_5_f | CCL4_cass_S_3_r | BAD | GOOD | BAD | BAD |
| CCL4 | short | CM020797 | 2 | 6 | CCL4_cass_S_5_f | CCL4_cass_S_4_r | BAD | GOOD | BAD | BAD |
| CD200R1 | short | CM020797 | 2 | 7 | CD200R1_cass_S_f | CD200R1_cass_S_3_r | BAD | GOOD | BAD | BAD |
| CD200R1 | short | CM020797 | 2 | 8 | CD200R1_cass_S_f | CD200R1_cass_S_4_r | BAD | BAD | BAD | BAD |
| CD79B | short | CM020797 | 2 | 9 | CD79B_cass_S_f | CD79B_cass_S_1_r | BAD | GOOD | BAD | BAD |
| CHRNA1 | long | CM020797 | 2 | 10 | CHRNA1_cass_L_f | CHRNA1_cass_L_r | BAD | BAD | BAD | BAD |
| CHRNA1 | long | CM020797 | 2 | 11 | CHRNA1_cass_L_1_f | CHRNA1_cass_L_r | BAD | GOOD | BAD | BAD |
| CLEC12A | short | CM020797 | 2 | 12 | CLEC12A_cass_S_f | CLEC12A_cass_S_r | BAD | GOOD | BAD | BAD |
| CLEC12A | short | CM020797 | 3 | 1 | CLEC12A_cass_S_f | CLEC12A_cass_S_1_r | BAD | GOOD | BAD | BAD |
| CLEC4A | short | CM020797 | 3 | 2 | CLEC4A_cass_S_f | CLEC4A_cass_S_r | BAD | GOOD | BAD | BAD |
| CLEC4A | short | CM020797 | 3 | 3 | CLEC4A_cass_S_1_f | CLEC4A_cass_S_r | BAD | GOOD | GOOD | BAD |
| COL13A1 | long | CM020797 | 3 | 4 | COL13A1_cass_L_3_f | COL13A1_cass_L_3_r | BAD | GOOD | BAD | BAD |
| CTDSPL | short | CM020797 | 3 | 5 | CTDSPL_cass_S_1_f | CTDSPL_cass_S_r | GOOD | GOOD | GOOD | GOOD |
| DISC1 | short | CM020797 | 3 | 6 | DISC1_alt5_S_1_f | DISC1_alt5_S_r | BAD | GOOD | BAD | BAD |
| EDN3 | long | CM020797 | 3 | 7 | EDN3_alt5_L_f | EDN3_alt5_L_1_r | BAD | GOOD | BAD | BAD |
| ERBB2IP | short | CM020797 | 3 | 8 | ERBB2IP_cass_S_1_f | ERBB2IP_cass_S_r | BAD | GOOD | BAD | BAD |
| F11R | long | CM020797 | 3 | 9 | F11R_cass_L_f | F11R_cass_L_1_r | BAD | GOOD | BAD | BAD |
| FAM19A3 | long | CM020797 | 3 | 10 | FAM19A3_alt3_L_f | FAM19A3_alt3_L_r | BAD | GOOD | BAD | BAD |
| FCGR2B | long | CM020797 | 3 | 11 | FCGR2B_cass_L_1_f | FCGR2B_cass_L_r | BAD | BAD | BAD | BAD |
| FCN3 | long | CM020797 | 3 | 12 | FCN3_cass_L_f | FCN3_cass_L_r | BAD | GOOD | BAD | BAD |
| FCN3 | long | CM020818 | 4 | 1 | FCN3_cass_L_f | FCN3_cass_L_1_r | GOOD | GOOD | BAD | BAD |
| FLJ14154 | long | CM020818 | 4 | 2 | FLJ14154_alt5_L_f | FLJ14154_alt5_L_r | GOOD | GOOD | BAD | BAD |
| FLJ14154 | long | CM020818 | 4 | 3 | FLJ14154_alt5_L_f | FLJ14154_alt5_L_1_r | GOOD | BAD | GOOD | BAD |
| FLJ22222 | long | CM020818 | 4 | 4 | FLJ22222_cass_L_f | FLJ22222_cass_L_r | GOOD | GOOD | GOOD | GOOD |
| GIMAP6 | short | CM020818 | 4 | 5 | GIMAP6_alt3_S_f | GIMAP6_alt3_S_r | BAD | GOOD | BAD | BAD |
| GPR137 | short | CM020818 | 4 | 6 | GPR137_intron_S_f | GPR137_intron_S_r | BAD | BAD | BAD | BAD |
| GPR137 | short | CM020818 | 4 | 7 | GPR137_intron_S_1_f | GPR137_intron_S_r | BAD | BAD | BAD | BAD |
| GPR172B | short | CM020818 | 4 | 8 | GPR172B_alt3_S_f | GPR172B_alt3_S_r | BAD | GOOD | BAD | BAD |
| GRIA2 | short | CM020818 | 4 | 9 | GRIA2_alt5_S_f | GRIA2_alt5_S_1_r | BAD | GOOD | GOOD | BAD |
| HERC6 | short | CM020818 | 4 | 10 | HERC6_cass_S_f | HERC6_cass_S_1_r | GOOD | GOOD | GOOD | GOOD |
| HIF1A | short | CM020818 | 4 | 11 | HIF1A_cass_S_f | HIF1A_cass_S_1_r | GOOD | BAD | GOOD | BAD |
| HIG2 | long | CM020818 | 4 | 12 | HIG2_alt5_L_f | HIG2_alt5_L_r | GOOD | GOOD | BAD | BAD |
| HIG2 | short | CM020819 | 5 | 1 | HIG2_alt5_S_f | HIG2_alt5_S_1_r | GOOD | GOOD | GOOD | GOOD |
| HNRPD | short | CM020819 | 5 | 2 | HNRPD_cass_S_3_f | HNRPD_cass_S_4_r | GOOD | BAD | GOOD | BAD |
| ICAM4 | long | CM020819 | 5 | 3 | ICAM4_alt3_L_1_f | ICAM4_alt3_S_r | GOOD | GOOD | BAD | BAD |
| ICAM4 | short | CM020819 | 5 | 4 | ICAM4_alt3_S_f | ICAM4_alt3_S_r | BAD | GOOD | BAD | BAD |
| ICAM4 | short | CM020819 | 5 | 5 | ICAM4_alt3_S_f | ICAM4_alt3_S_1_r | BAD | GOOD | BAD | BAD |
| IGSF4 | short | CM020819 | 5 | 6 | CADM1_cass_S_f | IGSF4-del-exon84/33/54-BSP-Rev | BAD | GOOD | GOOD | BAD |
| IQCH | short | CM020819 | 5 | 7 | IQCH_cass_S_1_f | IQCH_cass_S_r | BAD | GOOD | BAD | BAD |
| ITGA6 | long | CM020819 | 5 | 8 | ITGA6_cass_L_1_f | ITGA6_cass_L_r | GOOD | BAD | GOOD | BAD |
| KIF13A | short | CM020819 | 5 | 9 | KIF13A_cass_S_2_f | KIF13A_cass_S_2_r | BAD | BAD | BAD | BAD |
| KLK8 | long | CM020819 | 5 | 10 | KLK8_alt3_L_f | KLK8_alt3_L_1_r | GOOD | GOOD | GOOD | GOOD |
| KLRD1 | long | CM020819 | 5 | 11 | KLRD1_cass_L_f | KLRD1_cass_L_r | GOOD | GOOD | GOOD | GOOD |
| KLRD1 | short | CM020797,CM020819 | 6,6 | 1,1 | KLRD1_cass_S_f | KLRD1_cass_S_1_r | BAD | GOOD | BAD | BAD |
| KLRD1 | short | CM020819 | 5 | 12 | KLRD1_cass_S_f | KLRD1_cass_S_r | BAD | GOOD | BAD | BAD |
| LOC348801 | long | CM020797,CM020819 | 6,6 | 2,2 | LOC348801_alt3_L_f | LOC348801_alt3_L_r | BAD | GOOD | BAD | BAD |
| LOC348801 | long | CM020797,CM020819 | 6,6 | 3,3 | LOC348801_alt3_L_f | LOC348801_alt3_L_1_r | BAD | GOOD | BAD | BAD |
| LOC642393 | long | CM020797,CM020819 | 6,6 | 4,4 | LOC642393_alt3_L_1_f | LOC642393_alt3_L_r | BAD | GOOD | BAD | BAD |
| LOC642393 | short | CM020797,CM020819 | 6,6 | 5,5 | LOC642393_alt3_S_f | LOC642393_alt3_S_r | BAD | GOOD | BAD | BAD |
| LOC642393 | short | CM020797,CM020819 | 6,6 | 6,6 | LOC642393_alt3_S_1_f | LOC642393_alt3_S_r | BAD | GOOD | GOOD | BAD |
| LOC643446 | short | CM020797,CM020819 | 6,6 | 7,7 | LOC643446_alt3_S_f | LOC643446_alt3_S_r | GOOD | GOOD | GOOD | GOOD |
| MEOX1 | short | CM020797,CM020819 | 6,6 | 8,8 | MEOX1_cass_S_f | MEOX1_cass_S_r | BAD | GOOD | BAD | BAD |
| METTL1 | short | CM020797,CM020819 | 6,6 | 9,9 | METTL1_cass_S_f | METTL1_cass_S_r | GOOD | BAD | GOOD | BAD |
| MPZL1 | long | CM020797,CM020819 | 6,6 | 10,10 | MPZL1_cass_S_f | MPZL1_cass_L_r | GOOD | GOOD | GOOD | GOOD |
| MPZL1 | long | CM020797,CM020819 | 6,6 | 11,11 | MPZL1_cass_S_1_f | MPZL1_cass_L_1_r | GOOD | GOOD | GOOD | GOOD |
| MPZL1 | short | CM020797,CM020819 | 6,6 | 12,12 | MPZL1_cass_S_f | MPZL1_cass_S_r | GOOD | BAD | GOOD | BAD |
| MPZL1 | short | CM020819 | 7 | 1 | MPZL1_cass_S_1_f | MPZL1_cass_S_r | GOOD | GOOD | GOOD | GOOD |
| MRPL47 | short | CM020819 | 7 | 2 | MRPL47_cass_S_2_f | MRPL47_cass_S_r | GOOD | GOOD | BAD | BAD |
| MRPL47 | short | CM020819 | 7 | 3 | MRPL47_cass_S_3_f | MRPL47_cass_S_r | GOOD | GOOD | BAD | BAD |
| MYH11 | long | CM020819 | 7 | 4 | MYH11_cass_S_f | MYH11_cass_L_r | GOOD | GOOD | GOOD | GOOD |
| MYH11 | long | CM020819 | 7 | 5 | MYH11_cass_S_f | MYH11_cass_L_1_r | GOOD | GOOD | GOOD | GOOD |
| NDRG2 | short | CM020819 | 7 | 6 | NDRG2_cass_S_2_f | NDRG2_cass_S_4_r | BAD | GOOD | BAD | BAD |
| NR4A2 | short | CM020819 | 7 | 7 | NR4A2_alt3_S_f | NR4A2_alt3_S_r | GOOD | GOOD | GOOD | GOOD |
| NR4A2 | short | CM020819 | 7 | 8 | NR4A2_alt3_S_f | NR4A2_alt3_S_1_r | GOOD | GOOD | GOOD | GOOD |
| NTRK2 | long | CM020819 | 7 | 10 | NTRK2_cass_L_1_f | NTRK2_cass_L_r | BAD | GOOD | BAD | BAD |
| NTRK2 | long | CM020819 | 7 | 9 | NTRK2_cass_L_f | NTRK2_cass_L_r | BAD | GOOD | BAD | BAD |
| NTRK2 | short | CM020819 | 7 | 11 | NTRK2_cass_S_f | NTRK2_cass_S_r | BAD | GOOD | BAD | BAD |
| P2RY6 | long | CM020819 | 7 | 12 | P2RY6_cass_L_1_f | P2RY6_cass_L_r | BAD | GOOD | BAD | BAD |
| PAX2 | long | CM020819 | 8 | 1 | PAX2_alt3_L_f | PAX2_alt3_L_r | GOOD | GOOD | GOOD | GOOD |
| PAX2 | short | CM020819 | 8 | 2 | PAX2_alt3_S_f | PAX2_alt3_S_r | GOOD | GOOD | GOOD | GOOD |
| PAX2 | short | CM020819 | 8 | 3 | PAX2_alt3_S_f | PAX2_alt3_S_1_r | GOOD | GOOD | GOOD | GOOD |
| PPHLN1 | long | CM020819 | 8 | 4 | PPHLN1_cass_L_2_f | PPHLN1_cass_S_1_r | GOOD | GOOD | GOOD | GOOD |
| PYHIN1 | long | CM020819 | 8 | 5 | PYHIN1_cass_L_f | PYHIN1_cass_L_r | BAD | GOOD | BAD | BAD |
| PYHIN1 | long | CM020819 | 8 | 6 | PYHIN1_cass_L_f | PYHIN1_cass_L_1_r | BAD | GOOD | BAD | BAD |
| PYHIN1 | short | CM020819 | 8 | 7 | PYHIN1_cass_S_f | PYHIN1_cass_S_r | BAD | GOOD | BAD | BAD |
| PYHIN1 | short | CM020819 | 8 | 8 | PYHIN1_cass_S_f | PYHIN1_cass_S_1_r | BAD | GOOD | BAD | BAD |
| RBMS1 | long | CM020819 | 8 | 9 | RBMS1_cass_L_f | RBMS1_cass_L_1_r | GOOD | GOOD | GOOD | GOOD |
| RREB1 | short | CM020819 | 8 | 10 | RREB1_cass_S_f | RREB1_cass_S_r | GOOD | GOOD | GOOD | GOOD |
| SCARF1 | short | CM020819 | 8 | 11 | SCARF1_alt3_S_f | SCARF1_alt3_S_r | BAD | BAD | BAD | BAD |
| SCARF1 | short | CM020819 | 8 | 12 | SCARF1_alt3_S_1_f | SCARF1_alt3_S_r | BAD | BAD | BAD | BAD |
| SEPT8 | long | CM020800 | 1 | 1 | SEPT8_alt3_L_1_f | SEPT8_alt3_L_1_r | GOOD | GOOD | GOOD | GOOD |
| SIRPB2andNSFL1C | long | CM020800 | 1 | 2 | SIRPB2andNSFL1C_alt5_S_f | SIRPB2andNSFL1C_alt5_L_r | BAD | GOOD | BAD | BAD |
| SLC25A45 | short | CM020800 | 1 | 3 | SLC25A45_cass_S_f | SLC25A45_cass_S_r | BAD | BAD | BAD | BAD |
| SLC30A2 | short | CM020800 | 1 | 4 | SLC30A2_cass_S_f | SLC30A2_cass_S_r | BAD | GOOD | BAD | BAD |
| SLC30A2 | short | CM020800 | 1 | 5 | SLC30A2_cass_S_f | SLC30A2_cass_S_1_r | BAD | GOOD | BAD | BAD |
| SPP1 | short | CM020800 | 1 | 6 | SPP1_cass_S_f | SPP1_cass_S_r | GOOD | BAD | BAD | BAD |
| SPP1 | short | CM020800 | 1 | 7 | SPP1_cass_S_1_f | SPP1_cass_S_r | GOOD | BAD | GOOD | BAD |
| TFEC | long | CM020800 | 1 | 8 | TFEC_cass_L_2_f | TFEC_cass_L_1_r | GOOD | BAD | BAD | BAD |
| TFEC | long | CM020800 | 1 | 9 | TFEC_cass_L_2_f | TFEC_cass_L_2_r | GOOD | GOOD | BAD | BAD |
| TMTC4 | short | CM020800 | 1 | 10 | TMTC4_cass_S_f | TMTC4_cass_S_r | GOOD | GOOD | GOOD | GOOD |
| TOM1L2 | short | CM020800 | 1 | 11 | TOM1L2_cass_S_1_f | TOM1L2_cass_S_r | BAD | BAD | BAD | BAD |
| TRAPPC6B | long | CM020800 | 1 | 12 | TRAPPC6B_cass_L_f | rs.TRAPPC6B.R1 | BAD | GOOD | BAD | BAD |
| TRAPPC6B | long | CM020800 | 2 | 1 | TRAPPC6B_cass_L_1_f | rs.TRAPPC6B.R1 | BAD | GOOD | BAD | BAD |
| VNN3 | long | CM020800 | 2 | 2 | VNN3_alt3_L_f | VNN3_alt3_L_r | BAD | BAD | BAD | BAD |
| VNN3 | long | CM020800 | 2 | 3 | VNN3_alt3_L_1_f | VNN3_alt3_L_r | BAD | GOOD | BAD | BAD |
| VNN3 | short | CM020800 | 2 | 4 | VNN3_alt3_S_f | VNN3_alt3_S_r | BAD | GOOD | BAD | BAD |
| VNN3 | short | CM020800 | 2 | 5 | VNN3_alt3_S_f | VNN3_alt3_S_1_r | BAD | GOOD | BAD | BAD |
| VPS24 | long | CM020800 | 2 | 6 | VPS24_cass_L_f | VPS24_cass_L_1_r | GOOD | BAD | BAD | BAD |
| ZDHHC13 | short | CM020800 | 2 | 7 | ZDHHC13_cass_S_f | ZDHHC13_cass_S_r | BAD | GOOD | BAD | BAD |
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