Table 1.
List of primer sequences
| gRNA competition assay | |
|---|---|
| Human gRNAs | Sequence |
| SRPK1 (1) | GGTGTGGATGATACGGCACT |
| SRPK1 (2) | CTGCATGGTATTTGAAGTTT |
| SRPK1 (3) | TTACCGGTCTCACCATGGAG |
| BRD4S-ex12-SA_A | TTTCTCTCTCCCTCTACGT |
| BRD4S-ex12-SA_B | TTAGGCAGGACCTACGTAG |
| BRD4_ET_domain | AGTCGATTTCAATCTCGTCG |
| BRD4_BD2_domain | GTAGAAGGGCCAGGCGTAGG |
| BCL2 Intergenic (1) | GAGTGTCTCAATGGGCAGCG |
| BCL2 Intergenic (2) | AAGAGCCACGGCCTAAAGCA |
| Mouse gRNAs | Sequence |
| Srpk1 (1) | ACCTGCAGACCCCGATGGTG |
| Srpk1 (2) | TGAATGAGCAGTACATTCGA |
| RT-PCR | ||
|---|---|---|
| Forward Primer | Reverse Primer | |
| HOXA9 | GAATGAGAGCGGCGGAGAC | GAGCGAGCATGTAGCCAGTTG |
| c-MYC | AATGAAAAGGCCCCCAAGGTAGTTATCC | GTCGTTTCCGCAACAAGTCCTCTTC |
| BCL2 | CTGCACCTGACGCCCTTCACC | CACATGACCCCACCGAACTCAAAGA |
| BRD4 | CTCCTCCTAAAAAGACGAAGA | TTCGGAGTCTTCGCTGTCAGAGGAG |
| GAPDH | GATGCCCTGGAGGAAGTGCT | AGCAGGCACAACACCACGTT |
| RIP qPCR | ||
|---|---|---|
| Forward Primer | Reverse Primer | |
| BRD1 | ACATCCCATGGACTTTGCCACA | CTCACCGCGGCTCTATAGAACA |
| BRD4 | CTCCTCCTAAAAAGACGAAGA | TTCGGAGTCTTCGCTGTCAGAGGAG |
| MYB | AGCACCGATGGCAGAAAGTACT | TCTCCCCTTTAAGTGCTTGGCA |
| MED24 | AGGAGCTCAAGTGGACAGCTTT | GGTGAGCTTCAGCAGGAACTCA |
| ChIP qPCR | ||
|---|---|---|
| Forward Primer | Reverse Primer | |
| BCL2 | ACAGCGCCAACAGAACTACT | CCCCACAACGGAGCTGTAAT |
| MYC | CAAGCTCTCCACTTGCCCCT | GCCCTGAGATGTGTCTGCCT |
| EZH2 | CTTCTGAGTCCCACCGGGTG | GCCGTGTGTTCAGCGAAAGA |
| DUSP6 | GTAGAGGAAGGTCGGGGAGA | CACACAGGGCCATCTCAACT |
| DGKI | GCCACCCCCTCATCTCTCAC | TCTTCCAAGGACCCAGGGGA |
| Splicing Validation – RT-qPCR | ||
|---|---|---|
| Exon Skipping | Forward Primer | Reverse Primer |
| BRD1 (Exons 11-12) | AATGTCACTGAGGTCGCTGG | ACGTGCTGAAGATTGGGGAG |
| BRD4-Long (Exons 10-12) | TCGGAGCCATCTCTGTTTC | CGACTTTGAGACCCTGAAGC |
| BRD4-Short (Exons 10-12) | AATGATTAGGCAGGACCTGTT | CGACTTTGAGACCCTGAAGC |
| Exon Inclusion | Forward Primer | Reverse Primer |
| MYB (Exon 8-Intron 8) | TGAGCTAAAAGGACAGCAGGT | CAAAGCACAAGGAGCCATC |
| Alternative 5' Splice Site | Forward Primer | Reverse Primer |
| PIM1 (Exon 4-Intron 4) | CGACATCAAGGACGAAAACA | AGACACCCACACCCTTTCCT |
| Intron Retention | Forward Primer | Reverse Primer |
| MED24 (Exon 6-Intron 6) | AAGTCCCTGGGATGTGTGC | CTGGAGAAAACCCTCAGCAG |
| KAT5 (Exon 1- Intron 1) | CGGAACCAGGACAACGAAGA | ACCTCTCGGAGCAGCTAAGA |
| METTL3 (Exon 9-Intron 8) | AGACCCTGGTTGAAGCCTTG | TGGGGCCCAATTCAATAGGT |
| VEGFA (Exon 5-Intron 5) | ACCAAAGAAAGATAGAGCAAGACAA | ATTGTTGCTGCCACCACAAG |
| MED16 (Exon 14-Intron 14) | GACTTGAGCATGGTGACACAG | AAAGTGGGGCAGGCGTAA |
| PRMT5 (Exon 12-Intron 11) | CACCCATTCCCTCATGTCTG | TTTCCTTAACATCTCTCCTTACCTT |