|
| Status |
Public on Dec 31, 2023 |
| Title |
Root 2.0 mM Nitrogen (mild limitation), Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Panicum virgatum |
| Characteristics |
tissue: Root
genotype: WT cv. Alamo
treatment: N limitation (mild)
|
| Treatment protocol |
Plants were watered daily to field capacity during a 4-week growth period with a modified nutrient solutions
|
| Growth protocol |
Germinated seedling were growth in cones (6.9 cm in diameter X 25.4 cm in depth) filled with 40% all-purpose sand, 40% Q-ROK silica sand and 20% fine (2-4 mm particle size) perlite.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a cetyltrimethylammonium bromide (CTAB) and LiCl method (Chang, Puryear, & Cairney, 1993). RNA was treated with DNase I to remove genomic DNA.
RNA libraries were prepared using Illumina TruSeq RNA library preparation kit following manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
N2_R2
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped using to reference genome (v4.1) using HISAT2 2.0.5 and Stringtie 1.2.4 using default parameters.
Read count extraction and normalization were performed using Cuffdiff software.
Assembly: Panicum virgatum v4.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 13, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Raul Huertas |
| E-mail(s) |
[email protected]
|
| Organization name |
The James Hutton Institute
|
| Department |
Environmental and Biochemical Sciences
|
| Street address |
Errol Road
|
| City |
Invergowrie / Dundee |
| State/province |
Perth and Kinross |
| ZIP/Postal code |
DD2 5DA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24761 |
| Series (1) |
| GSE237286 |
Transcriptional, Metabolic, Physiological and Developmental Responses to Nitrogen Limitation in Switchgrass (Panicum virgatum) |
|
| Relations |
| BioSample |
SAMN36437653 |
| SRA |
SRX21012271 |
