|
| Status |
Public on Dec 11, 2018 |
| Title |
15143-29_2141 |
| Sample type |
SRA |
| |
|
| Source name |
15143-29_foliage from field-grown plants
|
| Organism |
Solanum tuberosum |
| Characteristics |
genotype/variety: 15143 diploid mapping population clone
clone id: 15143-29
tissue: foliage from field-grown plants
run: RunB
adapter b barcode: CTC
channel: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The smallest leaflet from the 4th fully expanded compound leaf was removed from each of the five plants per plot and pooled for each replicate plot. Leaf tissue was ground in the Lysing Matrix D tubes using a Geno Grinder 2000 (SPEX CertiPrep) machine for 2 min at speed 5. Samples were kept frozen. One ml RNA lysis buffer (200 mM sodium borate decahydrate (Borax), pH 9.0, 30 mM ethylene glygol bis (aminoethyl ether)-N-N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), and 10 mM dithiothreitol) plus 1 % (w/v) sodium deoxycholate and 2% (w/v) polyvinylpyrrolidone (PVP) (Mr 40,000)) was added to ground leaf tissue in each tube.
Template DNA hybridization and sequencing on an Illumina Genome Analyzer II (Illumina, San Diego, USA) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
*_arn*.txt: Adapter and barcode sequences were trimmed
*1x3.txt: Sequences that were not present in at least one of the three replicates were removed (1X3 tags)
Tag count data were transformed into a data matrix using in-house Perl scripts and transformed to the relative unit of counts per million.
Supplementary_files_format_and_content: tab delimited txt file with tag sequence and tag counts
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
Dec 11, 2018 |
| Contact name |
Helen H. Tai |
| E-mail(s) |
Helen.Tai@canada.ca
|
| Phone |
506 460 4519
|
| Organization name |
Agriculture and Agri-Food Canada
|
| Department |
Potato Research Centre
|
| Street address |
P. O. Box 20280, 850 Lincoln Rd.
|
| City |
Fredericton |
| State/province |
New Brunswick |
| ZIP/Postal code |
E3B 4Z7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13899 |
| Series (1) |
| GSE107936 |
Verticillium dahliae disease resistance and the regulatory pathway for maturity and tuberization in potato |
|
| Relations |
| BioSample |
SAMN08160971 |
