To provide a reference transcript set for white clover, cDNA from mixed above-ground material of a single pot-grown plant of the inbred line S1 was subjected to sequencing on the Roche GS_FLX platform using Titanium sequencing chemistry, generating a total of 768,512 cleaned reads (mean length 300.21 nt).
After 23 weeks (duplicate experiments initiated in February 2010), the above ground plant material was harvested from half of the potting bags and aliquots of the topsoil, coal discard/topsoil (3:1, v/v), and coal discard substrates sampled using a PVC auger (30 × 2 cm) inserted to a depth of 10 cm and the cored samples oven dried (50 °C × 24 h) prior to HS analysis.
Affymetrix ATH1 microarrays were hybridized with labelled cRNA prepared from above ground plant material.
For a global view of small RNAs expressed in Chinese cabbage, we chose to collect material from the above ground portions of HT and MT seedlings and sequenced RNA fractions of 9 to 36 nucleotides (nt), using Illumina Genome Analyzer and mirVana™ miRNA Isolation Kit (Ambion, Inc).
At harvest, above ground plant material was cut, and roots were isolated from the soil and carefully washed in DI water to remove all visible soil.
The essential oils were obtained by hydrodistillation or extraction with dichloromethane (a new procedure we developed trying to obtain better, more separated compounds) from air dried above ground plant material and analyzed by GC-MS.
Above ground, girls as young as 10 were sorting mica from other mined material.
For S1, RNA was extracted from a mixed tissue sample (including leaves, stems, stolons and flowers) of above ground parts of a plant grown pot that was placed in darkness for 24 hrs prior to material collection.
These data do not tell the entire story, however, because the amount of available plant material (standing crop) is often 10 to 25 times greater below ground than it is above ground.
