Transcriptomes
RNA-Seq datasets for multiple species are available. MiSeq and HiSeq reads from multiple libraries were cleaned with Trimmomatic and assembled by Trinity. CD-hit was used to collapse highly similar reads into a single sequence. Older transcriptomes were built with SeqMan Pro.
Transcriptome | Date Run | Status | Organism | Program | Transcripts |
|---|---|---|---|---|---|
| Red Oak Ozone | 10-10-2011 | archived | Quercus rubra (Northern Red Oak) | Trinity | 45,857 |
| Quercus rubra 120313 | 12-03-2013 | current | Quercus rubra (Northern Red Oak) | Trinity; CD-HIT-EST | 52662 |
| Quercus rubra 081508 | 08-15-2008 | archived | Quercus rubra (Northern Red Oak) | SeqManPro | 28041 |
| Quercus alba 081508 | 08-15-2008 | current | Quercus alba (White Oak) | SeqManPro | 22102 |
| Prunus serotina 9-30-12 | 09-30-2012 | current | Prunus serotina (Black Cherry) | Newbler | 28,461 |
| Nyssa sylvatica 120313 | 12-03-2013 | archived | Nyssa sylvatica (Blackgum) | Trinity; CD-HIT-EST | 55630 |
| Nyssa sylvatica 101314 | 10-13-2014 | current | Nyssa sylvatica (Blackgum) | Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST | 138819 |
| Liriodendron tulipifera 120313 | 12-03-2013 | archived | Liriodendron tulipifera (Tulip Poplar) | Trinity; CD-HIT-EST | 53346 |
| Liriodendron tulipifera 101314 | 10-13-2014 | current | Liriodendron tulipifera (Tulip Poplar) | Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST | 58249 |
| Liquidambar styraciflua 010515 | 01-05-2015 | current | Liquidambar styraciflua (American Sweetgum) | Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST | 127406 |
| Juglans nigra 120313 | 12-03-2013 | current | Juglans nigra (Black Walnut) | Trinity; CD-HIT-EST | 78834 |
| Hydrangea_macrophylla_12072016 | 12-07-2016 | current | Hydrangea macrophylla (Hydrangea) | Newbler (Roche) | 42682 |
| Green Ash Ozone | 12-19-2012 | archived | Fraxinus pennsylvanica (Green Ash) | Trinity | 63,113 |
| Gleditsia triacanthos 082614 | 08-26-2014 | current | Gleditsia triacanthos (Honeylocust) | Trinity; CD-HIT-EST | 56845 |
| Fraxinus pennsylvanica 120313 | 12-03-2013 | current | Fraxinus pennsylvanica (Green Ash) | Trinity; CD-HIT-EST | 107611 |
| Fraxinus excelsior 08-02-16 | 08-02-2016 | current | Fraxinus excelsior (European Ash) | Maker, Augustus | |
| Fagus grandifolia 081508 | 08-15-2008 | current | Fagus grandifolia (American Beech) | SeqManPro | 8319 |
| Cornus_florida_12062016 | 12-06-2016 | current | Cornus florida (Dogwood) | Newbler (Roche) | 43158 |
| Castanea dentata 081508 | 08-15-2008 | current | Castanea dentata (American Chestnut) | SeqManPro | 45288 |
| Black Walnut Ozone | 12-19-2012 | archived | Juglans nigra (Black Walnut) | Trinity | 61,770 |
| Alnus rubra 021816 | 02-18-2016 | current | Alnus rubra (Red Alder) | Trinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST | 29113 |
| Alnus rhombifolia 021816 | 02-18-2016 | current | Alnus rhombifolia (White Alder) | Trinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST | 26186 |
| Acer saccharum 022416 | 02-24-2016 | current | Acer saccharum (Sugar Maple) | Trinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST | 117861 |
| Acer saccharum 010515 | 01-05-2015 | archived | Acer saccharum (Sugar Maple) | Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST | 128406 |
