|
| Status |
Public on Aug 02, 2024 |
| Title |
Epimedium pubescens leaves,LN,36d,rep A |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Epimedium pubescens |
| Characteristics |
tissue: leaves
treatment: Nitrogen deficiency
time: 36d
|
| Treatment protocol |
After 20 days of irrigation with 12.5% Hoagland nutrient solution for seedling recovery, seedlings with newly emerged roots and having resumed normal growth were subjected to different nitrogen levels: LN (nitrogen deficiency treatment, 0 mmol/L NO3-), MN (moderate nitrogen treatment, 7.5 mmol/L NO3-), and HN (excessive nitrogen treatment, 22.5 mmol/L NO3-).
|
| Growth protocol |
These seedlings were transplanted into cultivation pots filled with a substrate mixture of river sand and perlite (3:2), and then cultured in a greenhouse. The light intensity was maintained at 2000 luX for 14 hours per day, and the temperature was controlled at 22 ± 2°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of leaves was extracted using the RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (QIAGEN, Germany).
RNA liprares for RNA-sed were prepared usIng NEBNext® Ultra RNA Library Prep Kit for Illumina®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
N20A
|
| Data processing |
Raw data in FASTQ format (raw reads) is processed using FASTP software and low-quality reads are filtered.
Align the obtained clean data to the reference genome using HISAT2 v2.0.5.
StringTie (1.3.3b) was used for new gene prediction.
featureCounts (1.5.0-p3) is used to calculate the reads mapped to each gene.
Assembly: IMPLAD_EP_1.0
Supplementary files format and content: txt file includes raw counts for each Sample
Supplementary files format and content: txt file includes FPKM values for each Sample
|
| |
|
| Submission date |
Jul 30, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
尚年 刘 |
| E-mail(s) |
[email protected]
|
| Phone |
18890044585
|
| Organization name |
中国医学科学院药用植物研究所
|
| Street address |
马连洼街道马连洼北路151号
|
| City |
北京 |
| State/province |
北京 |
| ZIP/Postal code |
100100 |
| Country |
China |
| |
|
| Platform ID |
GPL34251 |
| Series (1) |
| GSE273547 |
Transcriptome Responses to Different Nitrogen Levels Reveals Regulatory Networks for Icariin-Flavonoid Metabolism in Epimedium pubescens |
|
| Relations |
| BioSample |
SAMN42929948 |
| SRA |
SRX25521798 |
