Data · dataset · 2024
RNA-Seq data of R. agastum and R. irroratum
Listed in ScienceDB
R. agastum and R. irroratum from experimental field at National Forest Garden of GuiZhou province were employed in this paper.
Description
Flower samples during the four developmental stages (S1-S4) were sheared and harvested. According to instructions of RNA pure Plant Kit (CWBIO, China), total RNA was extracted from flowers of R. agastum and R. irroratum.
RNA concentration and integrity was identified through Nanodrop spectrophotometer (Life Technologies, USA) and bioanalyzer 2100 (Agilent, USA) respectively. cDNA libraries preparation were finished via Biomarker Technology (Beijing, China) and then subjected to sequence using Illumina HiSeq X™ Ten platform. The high-quality clean reads/data were generated by removing the low-quality, adapter- and N-base reads, and assembled basing on the genome of Rhododendron delavayi assessed by Rhododendron plant Genome Database (RPGD, bioinfor.kib.ac.cn/RPGD/index.html).
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Function of the assembled unigene was annotated against the following database: KEGG (Kyoto Encyclopedia of Genes and Genomes); PFAM (protein family); Nt (non-redundant nucleotide sequences, NCBI); Swiss-Prot (a protein sequence database); Nr (non-redundant protein sequences, NCBI); KO (Kyoto Encyclopedia of Genes and Genomes Ortholog database); GO (Gene Ontology); and COG (Clusters of Orthologous Groups of proteins).
To normalize the gene expression level, FPKM (Fragments Per Kilobase of transcriptome per Million mapped reads) method was selected. Differential expression analysis of two groups (Ra and Ri) was conducted using DESeq2 package with the screening parameters: fold change ≥2 and FDR (false discovery rate) < 0.01 to identify the genes expressed significantly different. Meanwhile, GO and KEGG enrichment analysis were applied for analyzing the biological function of DEGs through using TopGO and KOBAS.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.16793 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Crop and pasture production 70% · RNA sequencing 65%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.16793 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3004 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (70%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |