|
| Status |
Public on Sep 24, 2014 |
| Title |
NonDorm022406 |
| Sample type |
SRA |
| |
|
| Source name |
Meristems excised from nondormant potato tubers in spring 2006
|
| Organism |
Solanum tuberosum |
| Characteristics |
cultivar: Russet Burbank
tissue: Non-dormant meristem
|
| Treatment protocol |
Dormant tubers mersitems were harvested approximately two weeks after harvest. Nondormant tubers mmeristesm were harvested from tubers stored at 4 C until peeping.
|
| Growth protocol |
Plants were field grown in the Red River Valley in North Dakota. Tubers were mechanically harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Meristems were excised with a micro curette, 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 |
| |
|
| 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 t 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 23, 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) |
| GSE61690 |
Transcriptional changes in dormant and non_dormant potato meristems |
|
| Relations |
| BioSample |
SAMN03076269 |
| SRA |
SRX708859 |
