Data from Lunardon et al. (2020)
Data from Lunardon et al. (2020)Version v1.1 of Gossypium hirsutum cv. Texas Marker-1 from CottonGen
Click links below to show sub-sets of annotations
| ShortStack | miRBase21-BestBlastHit | Yin_et_al_2012 | Xie_et_al_2015 | |
| MIRNA | 189 | 35 | 0 | 0 |
| nearMIRNA | 188 | 6 | 0 | 0 |
| siRNA20 | 52 | 2 | 0 | 0 |
| siRNA21 | 1,569 | 10 | 2 | 1 |
| siRNA22 | 1,761 | 1 | 0 | 0 |
| siRNA23 | 278 | 0 | 0 | 0 |
| siRNA24 | 130,188 | 37 | 0 | 0 |
| OtherRNA | 8,096 | 3 | 0 | 0 |
| NotExpressed | 0 | 6 | 0 | 0 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| hirsutum_all_reference_set | 646,402,452 | 279,360,612 | none | 1 | mixed | mixed | mixed | refset1 | 1 | merge of 66 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| GSM699074 | 8,420,059 | 7,215,061 | GEO | 0 | root | Yi- 11 | wt | A | 1 | root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with water |
| SRR651109 | 10,595,657 | 2,704,544 | SRA | 0 | anther | Dong A | genetic male sterility mutant | AA | 1 | anther (tetrad stage) -- control conditions |
| SRR651110 | 10,969,088 | 2,745,537 | SRA | 0 | anther | Dong A | genetic male sterility mutant | AB | 1 | anther (uninucleate stage) -- control conditions |
| SRR959502 | 4,245,482 | 1,379,166 | SRA | 0 | seedling | TM-1 | wt | AC | 1 | seedling (2-weeks-old plants post-emergence) -- control conditions |
| SRX1502642 | 17,852,577 | 15,947,478 | SRA | 0 | cotyledon | HR | wt | AD | 1 | cotyledon -- collected 24h after infestation with whitefly |
| SRX1502643 | 15,953,458 | 12,333,501 | SRA | 0 | cotyledon | ZS | wt | AE | 1 | cotyledon -- control conditions |
| SRX1502644 | 15,251,786 | 11,123,679 | SRA | 0 | cotyledon | ZS | wt | AF | 1 | cotyledon -- collected 24h after infestation with whitefly |
| SRX2362115 | 34,647,033 | 12,856,381 | SRA | 0 | cotyledon | HR | wt | AG | 1 | cotyledon -- control conditions |
| SRX611311 | 2,867,912 | 3,009,922 | SRA | 0 | leaf | Nan Dan Ba Di Da Hua | wt | AH | 1 | leaf (17-days-old plants) -- control conditions |
| SRX611312 | 3,074,560 | 3,405,761 | SRA | 0 | leaf | Nan Dan Ba Di Da Hua | wt | AI | 1 | leaf (17-days-old plants) -- collected 4h after salt stress |
| SRX611313 | 2,969,042 | 3,717,734 | SRA | 0 | leaf | Nan Dan Ba Di Da Hua | wt | AJ | 1 | leaf (17-days-old plants) -- collected 24h after salt stress |
| GSM699075 | 8,039,778 | 7,708,130 | GEO | 0 | root | Yi- 11 | wt | B | 1 | root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with Verticillium dahliae VJ37 |
| SRR080704 | 6,418,584 | 1,500,877 | SRA | 0 | fiber | TM-1 | wt | C | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR1586235 | 11,884,520 | 7,569,573 | SRA | 0 | leaf | TM-1 | wt | D | 1 | leaf (young) -- control conditions |
| SRR1586236 | 13,925,654 | 9,240,791 | SRA | 0 | leaf | TM-1 | wt | D | 1 | leaf (young) -- control conditions |
| SRR1586237 | 12,363,812 | 7,910,675 | SRA | 0 | leaf | TM-1 | wt | D | 1 | leaf (young) -- control conditions |
| SRR1586238 | 22,274,765 | 8,152,281 | SRA | 0 | ovule | TM-1 | wt | E | 1 | ovule (0 days post anthesis) -- control conditions |
| SRR1586239 | 15,583,091 | 6,014,781 | SRA | 0 | ovule | TM-1 | wt | E | 1 | ovule (0 days post anthesis) -- control conditions |
| SRR1586240 | 27,769,446 | 9,785,523 | SRA | 0 | ovule | TM-1 | wt | E | 1 | ovule (0 days post anthesis) -- control conditions |
| SRR1586241 | 19,976,752 | 4,334,671 | SRA | 0 | fiber | TM-1 | wt | F | 1 | fiber (14 days post anthesis) -- control conditions |
| SRR1586242 | 18,556,899 | 4,730,691 | SRA | 0 | fiber | TM-1 | wt | F | 1 | fiber (14 days post anthesis) -- control conditions |
| SRR1586243 | 21,437,428 | 5,462,888 | SRA | 0 | fiber | TM-1 | wt | F | 1 | fiber (14 days post anthesis) -- control conditions |
| SRR2032485 | 9,434,113 | 2,393,048 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | G | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032486 | 9,267,167 | 2,334,335 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | G | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032487 | 9,195,373 | 2,394,153 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | G | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032488 | 9,668,647 | 2,388,616 | SRA | 0 | shoot apex | 3798 | wt | H | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032489 | 9,480,662 | 2,716,577 | SRA | 0 | shoot apex | 3798 | wt | H | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032490 | 9,536,015 | 2,263,228 | SRA | 0 | shoot apex | 3798 | wt | H | 1 | shoot apex (seedling stage with 2 leaves) -- control conditions |
| SRR2032491 | 7,799,481 | 3,909,297 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | I | 1 | shoot apex (pre-budding stage with 6 leaves) -- control conditions |
| SRR2032492 | 7,996,368 | 3,851,215 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | I | 1 | shoot apex (pre-budding stage with 6 leaves) -- control conditions |
| SRR2032493 | 8,313,665 | 3,686,136 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | I | 1 | shoot apex (pre-budding stage with 6 leaves) -- control conditions |
| SRR2032494 | 7,459,405 | 3,528,088 | SRA | 0 | shoot apex | 3798 | wt | J | 1 | shoot apex (pre-budding stage with 5 leaves) -- control conditions |
| SRR2032495 | 7,996,153 | 4,009,046 | SRA | 0 | shoot apex | 3798 | wt | J | 1 | shoot apex (pre-budding stage with 5 leaves) -- control conditions |
| SRR2032496 | 7,556,343 | 3,597,677 | SRA | 0 | shoot apex | 3798 | wt | J | 1 | shoot apex (pre-budding stage with 5 leaves) -- control conditions |
| SRR2032497 | 9,039,627 | 2,259,692 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | K | 1 | shoot apex (budding stage with 8 leaves) -- control conditions |
| SRR2032498 | 8,557,890 | 2,589,927 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | K | 1 | shoot apex (budding stage with 8 leaves) -- control conditions |
| SRR2032499 | 9,310,693 | 2,432,269 | SRA | 0 | shoot apex | Huazhong 94-3130 | wt | K | 1 | shoot apex (budding stage with 8 leaves) -- control conditions |
| SRR2032500 | 8,121,840 | 3,122,305 | SRA | 0 | shoot apex | 3798 | wt | L | 1 | shoot apex (budding stage with 12 leaves) -- control conditions |
| SRR2032501 | 9,053,602 | 3,119,341 | SRA | 0 | shoot apex | 3798 | wt | L | 1 | shoot apex (budding stage with 12 leaves) -- control conditions |
| SRR2032502 | 7,062,664 | 4,004,050 | SRA | 0 | shoot apex | 3798 | wt | L | 1 | shoot apex (budding stage with 12 leaves) -- control conditions |
| SRR2217931 | 13,134,803 | 2,862,675 | SRA | 0 | ovule | TM-1 | wt | M | 1 | ovule (-3 -- -1 -- 0 -- 1 -- 3 -- 5 -- 10 -- 20 and 25 days post anthesis) -- control conditions |
| SRR2217933 | 14,239,313 | 3,149,216 | SRA | 0 | ovule | N1 | wt | N | 1 | ovule (-3 -- -1 -- 0 -- 1 -- 3 -- 5 -- 10 -- 20 and 25 days post anthesis) -- control conditions |
| SRR5149190 | 5,284,191 | 2,275,450 | SRA | 0 | fiber | Coker 312 | wt | O | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR5149194 | 5,408,952 | 2,870,233 | SRA | 0 | fiber | Coker 312 | wt | O | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR5149198 | 3,677,420 | 1,898,157 | SRA | 0 | fiber | Coker 312 | wt | O | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR5149191 | 2,965,272 | 2,097,732 | SRA | 0 | fiber | Coker 312 | wt | P | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149193 | 3,913,764 | 4,954,776 | SRA | 0 | fiber | Coker 312 | wt | P | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149197 | 4,222,464 | 3,416,934 | SRA | 0 | fiber | Coker 312 | wt | P | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149192 | 4,594,403 | 3,193,655 | SRA | 0 | fiber | Coker 312 | wt | Q | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149195 | 3,039,611 | 1,572,466 | SRA | 0 | fiber | Coker 312 | wt | Q | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149196 | 5,430,720 | 3,046,107 | SRA | 0 | fiber | Coker 312 | wt | Q | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149203 | 3,900,678 | 2,825,294 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | R | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149206 | 2,803,574 | 1,984,560 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | R | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149207 | 3,755,227 | 2,609,061 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | R | 1 | fiber (15 days post-anthesis) -- control conditions |
| SRR5149204 | 3,952,266 | 2,042,718 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | S | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149205 | 5,505,490 | 3,365,760 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | S | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149211 | 6,100,848 | 3,254,078 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | S | 1 | fiber (5 days post-anthesis) -- control conditions |
| SRR5149208 | 3,751,280 | 2,371,045 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | T | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR5149209 | 4,376,135 | 2,464,649 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | T | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR5149210 | 3,497,548 | 2,072,186 | SRA | 0 | fiber | Coker 312 | PHYA1 RNAi | T | 1 | fiber (10 days post-anthesis) -- control conditions |
| SRR576119 | 18,987,670 | 5,655,746 | SRA | 0 | hypocotyl | YZ1 | wt | U | 1 | hypocotyl (1-week-old plants -- 28 C in dark) -- control conditions |
| SRR576121 | 20,452,171 | 5,122,678 | SRA | 0 | embryogenic callus | YZ1 | wt | V | 1 | embryogenic callus (2 months after induction at 28 C in light) -- control conditions |
| SRR651105 | 11,051,884 | 2,995,277 | SRA | 0 | anther | Dong A | wt | W | 1 | anther (meiosis stage) -- control conditions |
| SRR651106 | 13,252,582 | 3,271,420 | SRA | 0 | anther | Dong A | wt | X | 1 | anther (tetrad stage) -- control conditions |
| SRR651107 | 10,507,168 | 2,448,674 | SRA | 0 | anther | Dong A | wt | Y | 1 | anther (uninucleate stage) -- control conditions |
| SRR651108 | 8,669,927 | 2,091,420 | SRA | 0 | anther | Dong A | genetic male sterility mutant | Z | 1 | anther (meiosis stage) -- control conditions |