|
| Status |
Public on May 08, 2023 |
| Title |
Replicate 3 of Small RNA-seq for alfalfa roots under normal conditions |
| Sample type |
SRA |
| |
|
| Source name |
roots
|
| Organism |
Medicago sativa |
| Characteristics |
tissue: roots
cell type: seedling
treatment: alkaline stress
time: CK
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Small RNA-seq for 14 days-old alfalfa roots under alkaline stress (50 mmol/L NaHCO3)
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Medicago sativa using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Medicago sativa
Supplementary files format and content: tab-delimited text files include known miRNA values for each Sample(All_samples_known_miRNA.txt)
Supplementary files format and content: tab-delimited text files include novel miRNA values for each Sample(All_samples_novel_miRNA.txt)
|
| |
|
| Submission date |
May 04, 2023 |
| Last update date |
May 08, 2023 |
| Contact name |
Lin Chen |
| E-mail(s) |
[email protected]
|
| Phone |
18701689845
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
Beijing, Haidian, West Road 2 yuanmingyuan.
|
| City |
Beijing |
| State/province |
Haidian |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL25536 |
| Series (2) |
| GSE231697 |
Small RNA-seq for alfalfa roots under alkaline stress |
| GSE231699 |
Alfalfa roots under alkaline stress |
|
| Relations |
| BioSample |
SAMN34337969 |
| SRA |
SRX20077666 |
