Table 1 |.
Primer and oligo sequences
| Primer name | Purpose | Sequence (5′–3′) | Reference |
|---|---|---|---|
| JUN-TSS forward | For checking R-ChIP enrichment (Step 60) | GGGTGACATCATGGGCTATT | |
| JUN-TSS reverse | For checking R-ChIP enrichment (Step 60) | TCGGACTATACTGCCGACCT | |
| JUN-TTS forward | For checking R-ChIP enrichment (Step 60) | AAATAAGCAGGCTGGGGAAT | |
| JUN-TTS reverse | For checking R-ChIP enrichment (Step 60) | CAATCAAGCATGGGGATAGG | |
| NEAT1-TSS forward | For checking R-ChIP enrichment (Step 60) | TAGTTGTGGGGGAGGAAGTG | |
| NEAT1-TSS reverse | For checking R-ChIP enrichment (Step 60) | ACCCTGCGGATATTTTCCAT | |
| NEAT1-TTS forward | For checking R-ChIP enrichment (Step 60) | AGAGGGAGGGAGAGCTGAAG | |
| NEAT1-TTS reverse | For checking R-ChIP enrichment (Step 60) | GCATGAAGTCAGACCAGCAA | |
| CLSPN-TSS forward | For checking R-ChIP enrichment (Step 60) | GGCTGAGGGAATCAGAGACA | 4 |
| CLSPN-TSS reverse | For checking R-ChIP enrichment (Step 60) | GGGCGTGTGCATAAACTCA | |
| CLSPN-TTS forward | For checking R-ChIP enrichment (Step 60) | GGCACACAGCTTGGAATGTA | |
| CLSPN-TTS reverse | For checking R-ChIP enrichment (Step 60) | CCCCAGCAACTCTGAGACAG | |
| PMS2-TSS forward | For checking R-ChIP enrichment (Step 60) | AGCTGAGAGCTCGAGGTGAG | 4 |
| PMS2-TSS reverse | For checking R-ChIP enrichment (Step 60) | GAGATCGCTGCAACACTGAG | |
| PMS2-TTS forward | For checking R-ChIP enrichment (Step 60) | GCCAGACGTTGAGGAAGAAG | |
| PMS2-TTS reverse | For checking R-ChIP enrichment (Step 60) | ATCAACCCTTCCACTGCTTG | |
| N9 random primera | For primer extension (Step 61) | 5′-/invddt/CAAGCAGAAGACGGCAT ACGAGNN NNNNNNN-3′ |
4 |
| Oligo Aa | For making an adaptor (Step 69) | 5′-/Phos/GATCGGAAGAGCGTC GTGTAGGGAAAGAGTGT-3′ | 4 |
| Oligo Ba | For making an adaptor (Step 69) | 5′-AGACGTGTGCTCTTCCGATCT-3′ | 4 |
| PCR primera | For PCR amplification (Step 74) | 5′-CAAGCAGAAGACGGCATACGAG −3′ | |
| Barcode primera | For PCR amplification (Step 74) | 5′-AATGATACGGCGACCACCGAGATCTACACNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ |
NNNNN, flexible barcode sequence; NNNNNNNNN, random sequence.
a
Oligonucleotides may need to be re-designed based on the specific sequencing platform. You may find the nxCode website (http://hannonlab.cshl.edu/nxCode/nxCode/main.html) useful for barcode sequence design. All oligonucleotides can be dissolved in H2O at a stock concentration of 10 μM and stored for at least 1 year at −80 °C.