PscLncRNA is a database for plant single-cell lncRNA analysis, which includes four species (Oryza sativa, Arabidopsis thaliana, Zea mays, Solanum lycopersicum). In the latest version, we only focused on intergenic lncRNAs (lincRNAs).
There are large number of lincRNAs from four different plant species in the latest version of PscLncRNA.
Different filtering criteria used in PscLncRNA.
All marker genes were identified using the function FindAllMarkers in the R package Seurat (v4.3.0.1), with the following parameters: “logfc.threshold = 0.25, min.pct = 0.25, only.pos = T”.
genomics distance < 5kb and expression correction > 0.5.
The R package hdWGCNA (v0.2.20) was used to construct weighted gene co-expression networks on scRNA-seq data with default parameters.
Hub genes are highly connected members of the co-expression network ranked by eigengene-based connectivity (kME) (Morabito et al., 2023). .
By using R packages Seurat and Harmony
Briefly, metacells are aggregates of small groups of similar cells originating from the same biological sample of origin.
We focused on intergenic lncRNAs (lincRNAs) to avoid the confusion of expression quantification which might be caused by genic lncRNAs or natural antisense lncRNAs and their parent mRNAs.
LincRNAs and mRNAs are co-expressed in the same functional networks identified by R package hdWGCNA (v0.2.20).
There are three main features in PscLncRNA, including Browse, Search and Visualization.
Find lincRNA detailed information in PscLncRNA.