Data from Lunardon et al. (2020)
Data from Lunardon et al. (2020)Version v4.04 of Solanum tuberosum cv. DM1-3 516 R44 from Spud DB
Click links below to show sub-sets of annotations
| ShortStack | miRBase21-BestBlastHit | |
| MIRNA | 122 | 86 |
| nearMIRNA | 117 | 21 |
| siRNA20 | 32 | 3 |
| siRNA21 | 3,159 | 28 |
| siRNA22 | 3,403 | 14 |
| siRNA23 | 78 | 2 |
| siRNA24 | 64,336 | 154 |
| OtherRNA | 5,334 | 24 |
| NotExpressed | 0 | 61 |
| accession | aligned reads | unaligned reads | source db | is refset? Alignments that are reference sets (value of 1) are mergers of other component libraries used to compile master small RNA annotations for a species. | tissue | ecotype / cultivar | genotype | replicate id Alignments that are biological replicates have the same replicate ids | refset id If set, the alignment is part of the indicated reference set | description |
|---|---|---|---|---|---|---|---|---|---|---|
| potato_all_reference_set | 359,253,616 | 258,923,093 | none | 1 | mixed | mixed | mixed | refset1 | 1 | merge of 50 libraries - reference set 1 |
| accession | aligned reads | unaligned reads | source db | is refset? Alignments that are reference sets (value of 1) are mergers of other component libraries used to compile master small RNA annotations for a species. | tissue | ecotype / cultivar | genotype | replicate id Alignments that are biological replicates have the same replicate ids | refset id If set, the alignment is part of the indicated reference set | description |
|---|---|---|---|---|---|---|---|---|---|---|
| GSM803582 | 3,085,153 | 1,018,369 | GEO | 0 | leaf | Kennebec | wt | A | 1 | leaf (72-days-old plants -- fully grown middle or upper leaf) -- control conditions |
| SRR4112347 | 8,304,621 | 10,984,136 | SRA | 0 | leaf | Pentland squire | wt | AA | 1 | leaf -- lineage P1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112350 | 2,932,245 | 7,042,833 | SRA | 0 | leaf | Pentland squire | wt | AB | 1 | leaf -- lineage P2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112353 | 5,997,656 | 7,909,557 | SRA | 0 | leaf | Pentland squire | wt | AC | 1 | leaf -- lineage P2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112354 | 5,324,373 | 5,905,350 | SRA | 0 | leaf | Pentland squire | wt | AD | 1 | leaf -- lineage P3 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112359 | 5,360,313 | 9,490,838 | SRA | 0 | leaf | Pentland squire | wt | AE | 1 | leaf -- lineage P3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112361 | 3,026,996 | 6,641,002 | SRA | 0 | leaf | Desiree | wt | AF | 1 | leaf -- lineage D2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112364 | 3,493,929 | 14,725,808 | SRA | 0 | leaf | Desiree | wt | AG | 1 | leaf -- lineage D2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR643260 | 14,580,981 | 5,004,047 | SRA | 0 | tuber | 10908-06 | wt | AH | 1 | tuber -- collected after 11 -- 12 -- 15 and 25 days at 20 C |
| SRR643261 | 19,364,666 | 5,509,588 | SRA | 0 | tuber | 10908-06 | wt | AI | 1 | tuber -- collected after 10 days at 20 C then 1 -- 2 -- 5 and 15 days at 4 C |
| SRR825901 | 2,103,755 | 524,791 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AJ | 1 | leaf (4-weeks-old plants) -- collected after 8 days at long day |
| SRR825902 | 4,359,364 | 963,633 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AJ | 1 | leaf (4-weeks-old plants) -- collected after 8 days at long day |
| SRX159043 | 2,690,968 | 652,947 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AJ | 1 | leaf (4-weeks-old plants) -- collected after 8 days at long day |
| SRX159038 | 2,942,702 | 613,974 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AK | 1 | leaf (4-weeks-old plants) -- collected after 8 days at short day |
| SRX159039 | 2,796,389 | 655,450 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AK | 1 | leaf (4-weeks-old plants) -- collected after 8 days at short day |
| SRX159040 | 2,803,009 | 635,224 | SRA | 0 | leaf | group Andigena clone ADG573 | wt | AK | 1 | leaf (4-weeks-old plants) -- collected after 8 days at short day |
| SRX159044 | 3,018,978 | 925,973 | SRA | 0 | stolon | group Andigena clone ADG573 | wt | AL | 1 | stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| SRX159045 | 3,842,009 | 1,167,175 | SRA | 0 | stolon | group Andigena clone ADG573 | wt | AL | 1 | stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| SRX159046 | 3,239,993 | 925,112 | SRA | 0 | stolon | group Andigena clone ADG573 | wt | AL | 1 | stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| SRX159049 | 2,820,645 | 682,371 | SRA | 0 | swollen stolon | group Andigena clone ADG573 | wt | AM | 1 | swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| SRX159047 | 3,449,017 | 926,589 | SRA | 0 | swollen stolon | group Andigena clone ADG573 | wt | AM | 1 | swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| SRX159048 | 2,568,028 | 712,622 | SRA | 0 | swollen stolon | group Andigena clone ADG573 | wt | AM | 1 | swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day |
| GSM803583 | 3,266,438 | 1,214,020 | GEO | 0 | flower | Kennebec -- Katahdin -- Pentland Ivory | wt | B | 1 | flower (72-days-old plants -- mature flower) -- control conditions |
| GSM803584 | 3,043,534 | 1,080,476 | GEO | 0 | stolon | unknown | wt | C | 1 | stolon (72-days-old plants -- stolon separated from tubers) -- control conditions |
| SRR1035225 | 21,623,611 | 6,184,560 | SRA | 0 | leaf | Kufri Chandramukhi | wt | D | 1 | leaf (45-days-old plants) -- control conditions |
| SRR1035226 | 18,811,023 | 5,572,648 | SRA | 0 | stem | Kufri Chandramukhi | wt | E | 1 | stem (45-days-old plants) -- control conditions |
| SRR1035227 | 18,355,350 | 6,084,370 | SRA | 0 | root | Kufri Chandramukhi | wt | F | 1 | root (45-days-old plants) -- control conditions |
| SRR1035228 | 23,870,330 | 6,972,320 | SRA | 0 | tuber | Kufri Chandramukhi | wt | G | 1 | tuber (45-days-old plants -- stage 0) -- control conditions |
| SRR1035229 | 23,266,101 | 6,868,207 | SRA | 0 | tuber | Kufri Chandramukhi | wt | H | 1 | tuber (45-days-old plants -- stage 1) -- control conditions |
| SRR1035230 | 24,513,870 | 6,533,882 | SRA | 0 | tuber | Kufri Chandramukhi | wt | I | 1 | tuber (45-days-old plants -- stage 2) -- control conditions |
| SRR1035231 | 23,748,300 | 6,833,699 | SRA | 0 | tuber | Kufri Chandramukhi | wt | J | 1 | tuber (45-days-old plants -- stage 3) -- control conditions |
| SRR1068585 | 8,371,916 | 8,230,686 | SRA | 0 | leaf | Zihuabei | wt | K | 1 | leaf (50-days-old plants -- entire plant leaves) -- control conditions |
| SRR1103932 | 8,335,535 | 8,016,813 | SRA | 0 | leaf | Zihuabei | wt | L | 1 | leaf (30-days-old plants -- entire plant leaves) -- PEG-induced drought stress for 20 days |
| SRR3341159 | 2,885,166 | 1,559,828 | SRA | 0 | leaf | unknown | wt | M | 1 | leaf (8-weeks-old plants) -- shifted to dark for 3 days |
| SRR3341161 | 3,085,926 | 1,961,867 | SRA | 0 | leaf | unknown | wt | N | 1 | leaf (8-weeks-old plants) -- shifted to dark for 3 days and exposed to red light for 12 --24 --and 48 h |
| SRR3341162 | 4,788,687 | 854,985 | SRA | 0 | microtuber | unknown | wt | O | 1 | microtuber (8-weeks-old plants) -- dark conditions |
| SRR3341163 | 4,240,882 | 919,425 | SRA | 0 | microtuber | unknown | wt | P | 1 | microtuber (8-weeks-old plants) -- exposed to red light for 12 -- 24 -- and 48 h |
| SRR4112323 | 5,099,836 | 10,901,395 | SRA | 0 | leaf | Pentland squire | wt | Q | 1 | leaf -- lineage source inoculum -- passage 0 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112334 | 3,718,549 | 8,167,342 | SRA | 0 | leaf | Pentland squire | wt | Q | 1 | leaf -- lineage source inoculum -- passage 0 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112324 | 2,560,955 | 5,507,715 | SRA | 0 | leaf | Desiree | wt | R | 1 | leaf -- lineage D3 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112328 | 4,612,742 | 8,046,678 | SRA | 0 | leaf | Desiree | wt | S | 1 | leaf -- lineage D3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112329 | 2,855,546 | 6,222,781 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | T | 1 | leaf -- lineage Dn1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112332 | 4,884,646 | 9,786,845 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | U | 1 | leaf -- lineage Dn1 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112333 | 2,716,160 | 7,307,036 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | V | 1 | leaf -- lineage Dn2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112337 | 5,006,327 | 7,703,222 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | W | 1 | leaf -- lineage Dn2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112338 | 6,664,031 | 10,255,152 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | W | 1 | leaf -- lineage Dn2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112342 | 8,775,819 | 8,741,545 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | X | 1 | leaf -- lineage Dn3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112345 | 2,101,789 | 5,175,810 | SRA | 0 | leaf | Desiree | wt | Y | 1 | leaf -- lineage D1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112356 | 4,925,229 | 10,598,138 | SRA | 0 | leaf | Desiree | wt | Y | 1 | leaf -- lineage D1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151 |
| SRR4112346 | 5,019,528 | 8,004,259 | SRA | 0 | leaf | NahG-Desiree | transformed with nahG gene | Z | 1 | leaf -- lineage DnxD1 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151 |