|
| Status |
Public on Dec 01, 2014 |
| Title |
NG_Four_days_after_exposure_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Periderm disc with apical meristem
|
| Organism |
Solanum tuberosum |
| Characteristics |
cultivar: Atlantic
agent: NG
time: Four days
|
| Treatment protocol |
Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine
|
| Growth protocol |
Commercially grown greenhouse minitubers (cv Atlantic)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One to two mm thick disc containing the apical bud was frozen in liquid N2. RNA was isolated using an Ambion RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine and harvest four days later
|
| Data processing |
Illumina software used for basecalling.
Sequence reads were trimmed for adaptor sequences and filtered using Galaxy with 100% of all reads having a minimum phred score of 20
Reads were mapped to the double monoploid DM1-3 516 R44 (DM1-3), Solanum tuberosum Grp. Phureja line (2n=24)
Reference genome was PGSC_DM_v3_2.1.11
Supplementary_files_format_and_content: tab delimited text file with FPKM values
|
| |
|
| Submission date |
Sep 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael A Campbell |
| E-mail(s) |
mac17@psu.edu
|
| Phone |
814-898-6474
|
| Organization name |
Penn State Erie
|
| Department |
School of Science
|
| Street address |
4205 College Drive
|
| City |
Erie |
| State/province |
PA |
| ZIP/Postal code |
16428 |
| Country |
USA |
| |
|
| Platform ID |
GPL13899 |
| Series (1) |
| GSE61796 |
Transcriptional changes in dormant potato minitubers treated with 1-(alpha-ethylbenzy)-3-nitroquanidine |
|
| Relations |
| BioSample |
SAMN03081359 |
| SRA |
SRX710698 |
