|
| Status |
Public on Mar 24, 2010 |
| Title |
Col/GxGF-IR rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root total RNA
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: C24
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.
|
| |
|
| Submission date |
Mar 05, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Krys Kelly |
| Organization name |
University of Cambridge
|
| Department |
Plant Sciences
|
| Lab |
Baulcombe Group
|
| Street address |
Downing Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 3EA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE20663 |
small RNAs sequences from grafted Arabidopsis thaliana and Nicotiana benthamiana tissues |
|
| Relations |
| SRA |
SRX017585 |
| BioSample |
SAMN00009795 |
