|
Status |
Public on Mar 24, 2010 |
Title |
Col/Col rep1 |
Sample type |
SRA |
|
|
Source name |
root total RNA
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col-0 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 |
SRX017566 |
BioSample |
SAMN00009776 |