ecotype: Col-dcl2,3,4 sample time: five weeks after grafting
Growth protocol
standard growth conditions (10hr light, 20 C)
Extracted molecule
total RNA
Extraction protocol
Total nucleic acid (TNA) extracts were prepared from pooled shoot and root samples derived from 3-4 individual grafts according to White and Kaper, 1989. To clone small RNAs, sRNAfractions were enriched from 12.5-25 µg of TNA using MirVana columns (Ambion) according to the manufacturer’s instruction. SRNAs were cloned by the Illumina sRNAcloning kit.
Library strategy
ncRNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
Illumina Genome Analyzer II
Description
Grafted plants are described using “shoot/root” notation
Data processing
Small RNA adapters were removed using an exact match to the sequence of the appropriate adapter. Reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.
