Table 10.
List of Primers Sequences and shRNA Sequences Used in this Research
| Real-time qPCR primers sequences | Sequence (5'→3') |
|---|---|
| HNRNPM sense | ctaacgcgagtgtatctcgag |
| HNRNPM anti-sense | cgctcccggctgcctccttgg |
| β-actin sense | GGGAAATCGTGCGTGACATTAAG |
| β-actin anti-sense | TGTGTTGGCGTACAGGTCTTTG |
| GAPDH sense | GGTCTCCTCTGACTTCAACA |
| GAPDH anti-sense | GTGAGGGTCTCTCTCTTCCT |
| MBD2a-Fwd | AGCAAGCCTCAGTTGGCAAGGT |
| MBD2a-Rev | TGTTCATTCATTCGTTGTGGGTCTG |
| MBD2c-Fwd | AGCAAGCCTCAGTTGGCAAGGT |
| MBD2c-Rev | TGAAAGCGCATGCCATGGTGCA |
| CTNNB1-Fwd | CAGAAGCTATTGAAGCTGAGG |
| CTNNB1-Rev | TTCCATCATGGGGTCCATAC |
| SNAI1-Fwd | TCGGAAGCCTAACTACAGCGA |
| SNAI1-Rev | AGATGAGCATTGGCAGCGAG |
| FZD3-Fwd | ATGGCTTTGAGATGGATTGTC |
| FZD3-Rev | GGCACATCCTCAAGGTTATAGGT |
| RBBP7-Fwd | TTGAGTGGACATCTCCTAAGTG |
| RBBP7-Rev | CCTGGTGTCCCATATCATAAGT |
| HDAC1-Fwd | CTTTAACCTGCCTATGCTGATG |
| HDAC1-Rev | CTCATTCGTGTTCTGGTTAGTC |
| HDAC2-Fwd | GCCCCATAAAGCCACTGCCGAAG |
| HDAC2-Rev | GCTCCAGCAACTGAACCGCCAG |
| MTA2-Fwd | GCCAAACCCTAACCAGATCA |
| MTA2-Rev | CAGGCATACCACTGAGCAGA |
| Flag-MBD2a-Fwd | GCTAGCATCGATACGCGTATGCGCGCGCACCCGG |
| Flag-MBD2a-Rev | TGCGGATCCTTCGAACTAGTTTAGGCTTCATCTCCACTGTCCATT |
| HA-MBD2c-Fwd | GCTAGCATCGATACGCGTATGCGCGCGCACCCGG |
| HA-MBD2c-Rev | TGCGGATCCTTCGAACTAGTTTATGGAGGAAAGGATTGGTTCTGCC |
| shRNAs | |
| MBD2a shRNA | CCGGGTAGCAATGATGAGACCCTTTCTCGAGAAAGGGTCTCATCATTGCTACT |
| HDAC1 shRNA | CCGGGCCGGTCATGTCCAAAGTAATCTCGAGATTACTTTGGACATGACCGGC |
| HDAC2 shRNA | CCGGCAGTCTCACCAATTTCAGAAACTCGAGTTTCTGAAATTGGTGAGACTGT |
| RBBP7 shRNA | CCGGCCTCCAGAACTCCTGTTTATTCTCGAGAATAAACAGGAGTTCTGGAGGT |
| MTA2 shRNA | GCCGGCGGACTTTCCTAATTGGAGTTCTCGAGAACTCCAATTAGGAAAGTCCGT |
| Control siRNA | UUCUCCGAACGUGUCACGUTT |
| OCT4 siRNA | AACAUGUGUAAGCUGCGGCCCdTdT |
| SOX2 siRNA | CUGCAGUACAACUCCAUGATT |
| MSP primers | |
| FZD3 MSP M-Fwd | GGAGAGGAGAAATATTTTTTAAGGAGTA |
| FZD3 MSP M-Rev | ACTCTAACCTACTACAAAACTCCAC |
| FZD3 MSP U-Fwd | AATATTTTTTAAGGAGTAAAATTGGG |
| FZD3 MSP U-Rev | ACTCTAACCTACTACTACAAAACTCCAC |
| MBD2_RIP_a_FWD | AAGCAAGCCTCAGTTGGCAAGGT |
| MBD2_RIP_a_REV | GAGAGGATCGTTTCGCAGTCTCTGT |
| MBD2_RIP_b_FWD | AAACAGAGACTGCGAAACGATCCTC |
| MBD2_RIP_b_REV | GGGTATGGGGACATGCACGGG |
| MBD2_RIP_c_FWD | TGCTGGGTACCTATAAAAGGGGCT |
| MBD2_RIP_c_REV | GCATGCCATGGTGCAGGACGA |
| ChIP assays primers sequences | Sequence (5'→3') |
| OCT4-HNRNPM Site sense | gatgcctcctctatcggactc |
| OCT4-HNRNPM Site anti-sense | cgtctgggctttgtgtgagcg |
| SOX2-HNRNPM Site sense | GTGATCCGCCGCCTCGGCCTCCCAT |
| SOX2-HNRNPM Site anti-sense | CTTGTTCAACCCGCGGTCCGGCACA |
| CTNNB1-OCT4 Site sense1 | ACTGGTTCATGTGGGGAAGGT |
| CTNNB1-OCT4 Site anti-sense1 | GGCTGGGGCAGCCCT |
| CTNNB1-OCT4 Site sense1 | AGGGATGGGCTGCCCCA |
| CTNNB1-OCT4 Site anti-sense1 | GGAGGAGGCCGGGAGCG |
| CTNNB1-SOX2 Site sense | ACCGTATGGCGTGTACCA |
| CTNNB1-SOX2 Site anti-sense | GAAGATGGCCGCCAGAT |
| E2F1-HNRNPM Site sense | GCCCAGACGCGGAGAAAA |
| E2F1-HNRNPM Site anti-sense | GCCGCTCTCTTCCTCCATTT |
| Antisense oligonucleotides sequences | |
| ASO ID | Sequence |
| ASO-1 | #T∗#C∗# G∗A∗T∗A∗C∗G∗A∗G∗A∗C∗C∗T∗C∗T∗G∗A∗A∗T∗T∗T∗ #T∗#C∗#T |
| ASO-2 | #T∗#C∗# G∗C∗C∗G∗A∗C∗A∗T∗C∗A∗A∗G∗A∗T∗G∗G∗A∗G∗A∗A∗ #T∗#C∗#T |
| ASO-3 | #T∗#C∗# C∗A∗T∗G∗G∗A∗G∗C∗G∗C∗A∗T∗T∗G∗G∗C∗T∗C∗T∗G∗ #T∗#C∗#T |
| Negative control | #T∗#C∗# T∗A∗T∗C∗G∗T∗G∗A∗T∗G∗T∗T∗ #T∗#C∗#T |
Note: # indicates LNA-modified nucleotides and ∗ indicates PTO linkages.
ASO, Antisense oligonucleotides; MSP, methylation-specific polymerase chain reaction; qPCR, quantitative polymerase chain reaction; shRNA, short hairpin RNA.