TABLE 1.
Genomic primer sets used for PCR amplification
| Primer name and type | Sequence (5′-3′) | Accession no.a |
|---|---|---|
| Oligonucleotides used for GREM procedure | ||
| LTR-specific primers | ||
| LTRfor1 | GTCTTGTGACCCTGACACATCC | |
| LTRfor2 | CCTCCATATGCTGAACGCTG | |
| LTRfor3 | GGGGCAACCCACCCCTAC | |
| Suppression adapter oligonucleotides | ||
| A1A2 | GTAATACGACTCACTATAGGGCAGTCGACGCGTGCCCGGTCCGAC | |
| A3 | GTCGGACCGGGC | |
| A1 | GTAATACGACTCACTATAGGGC | |
| A2 | AGTCGACGCGTGCCCGGTCCGAC | |
| A4 | TCGACGCGTGCCCGGTCCGACCT | |
| Oligonucleotides used for cap switch-based cDNA amplification | ||
| CDS | AAGCAGTGGTATCAACGCAGAGTAC(T)30 | |
| riboCS | TAACAACGCAGAGTACGCRGRGRG | |
| CS | TAACAACGCAGAGTACGCGG | |
| Primers used for RT-PCR experiments | ||
| LTR-specific primers | ||
| LTRfor1 | GTCTTGTGACCCTGACACATCC | |
| LTRfor2 | CCTCCATATGCTGAACGCTG | |
| LTRfor3 | GGGGCAACCCACCCCTAC | |
| Unique genomic primers specific to LTR 3′-flanking regions | ||
| gLTR62 | TAAGTGGATATAATTACTAAGTCCAGG | AC068381 |
| gLTR80 | CCAACATCTGTCTCTTCCCTG | AP002754 |
| gLTR81 | GACCATTTGCATGGACAAATC | AL451165 |
| gLTR99 | CCATCCCTTCCATGCCTTAG | AC069420 |
| gLTR100 | AGCTTTGTGGATTGTAATTTGG | AC072054 |
| gLTR108 | CTCAGTAAAGATGAAGGTATGACAAG | AL139421 |
| gLTR109 | GAGGCAGAGGTTGCAGTGAGCC | AC002400 |
| gLTR113 | ATAAAGGAGAAATCTTCCATGAAG | AC026424 |
| gLTR115 | TGTGACGGTATAATGGCCTCT | AC008648 |
| gLTR121 | TGCAATGTTCATGTTCGCTCC | AC012175 |
| gLTR129 | GGTTATGAATAAAGTTCCCTCGG | AC027750 |
| gLTR131 | AGAATAGAGCGAACAGACACAG | AL352982 |
| gLTR138 | AGGTTATTGATACATTGCATCGAC | AC023201 |
| gLTR139 | CAATAACAGTCATTCTCACTGGAG | AC118278 |
| gLTR140 | GAGTTGGGATGTGGTCTTAGG | AL353588 |
| gLTR141 | CTCATGCTAAACTGTCTGATTATGC | AC105049 |
| gLTR145 | TTGTGCAAACTGTCTACAGCCA | BC001407 |
| gLTR149 | AACATACAGGTTGAGGCCAGG | AC016577 |
| gLTR152 | TTGTAGCTGACCAACAGCCTGC | AC068213 |
| gLTR155 | TTAGGCCAGGGTCTCACTGAG | U47924 |
| HERV-K (HML-2) proviral gag gene-specific primer | ||
| Gag rev | AATGGCCCAATCATTCCATA | |
| Unique primers specific to known human genes | ||
| DOCK2 for | CCCAGGCATGGTAGGACCTATATTAGAG | AC008648 |
| DOCK2 rev | CGGTAATCCAGCAGCTTCTCCAG | AC008648 |
| BICD1 for | GCAGTCCCGACGCAGCAAAG | AC021108 |
| BICD1 rev | CTGTAGGTAGGAAGCCCCTGAAGTC | AC021108 |
| SLC4A8 for | CTGTTCCTGTACTGTGCCTGCATGTC | AC027750 |
| SLC4A8 rev | TGTAGCAGACAAGGGAACTGGCATC | AC027750 |
| C9orf39 for | AGTCAGCAGACAGAGCTAAATCCGAG | AC015640 |
| C9orf39 rev | GATCACTTTCTTTCTGGTCTTTTCCATC | AC015640 |
| GPR74 for | GGGCTGCAGTTCCTCACACAGG | AC055844 |
| GPR74 rev | GCTGGAGCTGGAAAGCTTCTTGG | AC055844 |
| RPL8 for | CCCGTGTGAAGCTGCCCTCC | AC130332 |
| RPL8 rev | TTGTCAATTCGGCCACCTCCAG | AC130332 |
| KLRB1 for | ATTGTTCCACCAAAGAATCCAGCC | AC006432 |
| KLRB1 rev | CACAGGTGTTAGTTCTTTTTGGCAGATC | AC006432 |
| TA-PP2C for | TGGGGATGGAGGTGTTCAGTGC | AC002350 |
| TA-PP2C rev | AGACATAAAGCCACACCAATCATCATAAC | AC002350 |
| MMP24 for | ACCATCGGAGAGGAAACACGAGC | AL121753 |
| MMP24 rev | CACCGTCACCTCCTTAAACACCCA | AL121753 |
| SLC25A16 for | GCCTTATTAATGGAACAGTCCTC | AC037456 |
| SLC25A16rev | TGAGGATCAGACTGCTTCTTGC | AC037456 |
| C6orf211 for | AGGTTATTGATACATTGCATCGAC | AL590543 |
| C6orf211 rev | CACGGTGAGTAGAACCATCTTG | AL590543 |
| AND-1 for | CACCATCACTTCCACAAGTCAC | AL352982 |
| AND-1 rev | AGAATAGAGCGAACCAGACACAG | AL352982 |
| SLB for | CCAATCGAGCCAGCTCTA | AC074117 |
| SLB rev | TACCGTAAAGGCAACGCATT | AC074117 |
| ZNF432 for | CATTGATAGCAGGTTGCTGTAGA | AC011468 |
| ZNF432 rev | AGAGTATCCCAGGTGCTGGC | AC011468 |
| FLJ21816 for | AGTTCTGGCAGTTGTGTCATCC | AC002400 |
| FLJ21816 rev | GGAAGCCTGATGAACTCGTCT | AC002400 |
| CEBPZ for | CTTGCTTGGAACACGTCATCA | AC007390 |
| CEBPZ rev | GTGTCCAGGCTTTAATGTTGCT | AC007390 |
| LIPH1 for | ACCGTGGACTCAACTCTGCATTCTC | AC069420 |
| LIPH1 rev | TAGTCCCAGCAGCCGCCCTC | AC069420 |
| SENP2 for | TCTAGGGACAAACCTATCACATTTACTCG | AC069420 |
| SENP2 rev | TTGTGTGGGTTGAACAGTCCAAAGC | AC069420 |
a
GenBank accession numbers of corresponding LTRs from nonredundant and high-throughout genome sequence databases.