|
| Status |
Public on Jun 21, 2016 |
| Title |
Atlantic_timepoint1_control1 |
| Sample type |
SRA |
| |
|
| Source name |
Atlantic_timepoint1_control_foliar tissue
|
| Organism |
Solanum tuberosum |
| Characteristics |
cultivar: Atlantic
treated with: 0 kg N ha-1 N-fertilizer
sampling date/time point: 2015-07-25
tissue: Foliar; apical leaflet of the last fully expanded leaf (usually the 4th leaf from the top of the plant)
|
| Treatment protocol |
The experiment included two fertilizer N rates in a randomized complete block design with four blocks. The control groups had no added ammonium nitrate. The treatment groups were fertilized with 180 kg ha^-1 of ammonium nitrate at planting.
|
| Growth protocol |
Plants were propagated in the field at the Potato Research Centre of Agriculture and Agri-Food Canada in New Brunswick. Plants were fertilized with 150 kg ha^-1 of P2O2 and K2O at planting. Hand cut 50g seed-pieces were hand-planted and imidaclorpid was applied to control for Colorado potato beetle. At each sampling, the apical leaflet of the last fully expanded leaf (usually the fourth leaf from the top of the plant) was sampled from each of 15 randomly selected plants in each plot and placed into 50 ml Falcon tubes. The tube was immediately placed in liquid N, and stored at -80 ˚C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissue was ground to a powder in liquid N using a mortar and pestle. Samples were pre-extracted in 1 ml Hot Borate Buffer (Wan & Wilkins 1994). The lysate supernatant (200 ul) was used for RNA extraction with the Biomek NXP Laboratory Automation Workstation (Beckman Coulter) using the RNAdvance Tissue Kit (Agencourt) according to the manufacturer’s instructions for liquid samples.
Libraries were generated using the TruSeq RNA kit (Illumina). Messenger RNA was purified from 1 g of total RNA using oligo-dT beads. The mRNA enriched fraction was reverse transcribed to generate cDNA fragments that were sheared to yield ~200 bp fragments. Following end-repair, 3’ end adenylation steps, and index ligation, a PCR amplification step was performed. A separate index was used for each N treatment-variety-replicate combination for a total of 24 indices.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: atlantic_time1_annotated_gene_exp.diff.gz
|
| Data processing |
Alignment with TopHat (-p 5 --library-type=fr-unstranded)
Transcript assembly with CuffLinks (--library-type=fr-unstranded --multi-read-correct --frag-bias-correct)
Assembly of reference transcriptome, per experiment, with CuffMerge
Differential expression analysis with CuffDiff (--multi-read-correct --frag-bias-correct). FPKM were calculated for all genes calculated as follow: exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Gene annotation added through custom perl script that took information from S. tuberosum ITAG1.0 gtf file (ftp://ftp.solgenomics.net/genomes/Solanum_tuberosum/annotation/ITAG1.0/).
Genome_build: S. tuberosum reference genome v3_2.1.10
Supplementary_files_format_and_content: gene_exp.diff, contains FPKM information for control samples vs. treatment, as well as a statistical test to determine whether each gene is differentially expressed between groups
|
| |
|
| Submission date |
Dec 11, 2015 |
| Last update date |
Sep 06, 2022 |
| Contact name |
Martina Stromvik |
| E-mail(s) |
[email protected]
|
| Phone |
+1 (514) 398 8627
|
| Fax |
+1 (514) 398 7897
|
| URL |
http://www.mcgill.ca/plant/faculty/stromvik/
|
| Organization name |
McGill University
|
| Department |
Department of Plant Science
|
| Lab |
Plant Bioinformatics
|
| Street address |
21,111 Lakeshore Rd
|
| City |
Ste-Anne-de-Bellevue |
| State/province |
Quebec |
| ZIP/Postal code |
H9X 3V9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16436 |
| Series (1) |
| GSE75926 |
The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs |
|
| Relations |
| BioSample |
SAMN04331818 |
| SRA |
SRX1478095 |
