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| Status |
Public on Mar 30, 2024 |
| Title |
Epimedium pubescens leaves,-P,90d,rep A [miRNA] |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Epimedium pubescens |
| Characteristics |
tissue: leaves
treatment: Phosphorus deficiency
time: 90d
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| Treatment protocol |
Irrigation was treated with adjusted Hogland's nutrient solution of 0 mmol/L and 1 mmol/L Pi.
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| Growth protocol |
The plants were cultivated in sand, under 2000 lux light for 14 hours daily, at 22 ± 2 ℃ in a controlled environment.
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| 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).2 ug of total RNA was used for the construction sequencing library.
Sequencing libraries were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (NEB E7300L). Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
P20A
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| Data processing |
To obtain clean reads from raw data in fastq format, custom Perl and Python scripts are employed for processing.
Bowtie is utilized to align small RNA tags against a reference sequence without mismatches. Using miRBase20.0 as the reference, modified versions of the software mirdeep2 and srna-tools-cli are applied to identify potential miRNAs and generate secondary structures.
To predict novel miRNAs, the available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) are integrated. These tools explore the secondary structures, Dicer cleavage sites, and minimum free energy of unannotated small RNA tags from previous steps.
Known and novel miRNAs in each sample are normalized for expression levels using TPM. Differential expression analysis is performed using DESeq2.
Assembly: IMPLAD_EP_1.0
Supplementary files format and content: XLS file includes raw counts for each Sample
Supplementary files format and content: XLS file includes TPM values for each Sample
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| Submission date |
Feb 28, 2024 |
| Last update date |
Mar 30, 2024 |
| Contact name |
尚年 刘 |
| E-mail(s) |
[email protected]
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| Phone |
18890044585
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| Organization name |
中国医学科学院药用植物研究所
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| Street address |
马连洼街道马连洼北路151号
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| City |
北京 |
| State/province |
北京 |
| ZIP/Postal code |
100100 |
| Country |
China |
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| Platform ID |
GPL34251 |
| Series (1) |
| GSE259444 |
Exploring the Dynamic Adaptive Responses of Epimedium pubescens to Phosphorus Deficiency Through Combined Transcriptome and miRNA Analysis [miRNA-Seq] |
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| Relations |
| BioSample |
SAMN40186787 |
| SRA |
SRX23776905 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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