The Circular RNome of Developmental and Injured spinal cord in Rat
We aim to uncover circular RNAs in nervous system particular in spinal cord during the development and injury. We analyzed 15 RNA-Seq datasets with 217 samples from rat and 7 RNA-Seq datasets with 94 samples from mouse using the same analysis pipeline. We employed CIRCexplore3 pipeline to identify circRNAs and quantified the expression of both circRNAs and linear RNAs. Linear annotation for rat was downloaded from the Ensembl (mRatBN7.2, v109) and linear annotation for mouse was downloaded from the GenCode (vM27).
This shiny application (Circular RNome in Rat, "CiRNat") was developed for exploration of indivisual circRNA or circRNAs from a loci and expression information across different datasets.
Dataset information
Note: nSample indicated number of samples analyzed instead of the total samples described in the original publication;nCircRNA_cut2 indicated number of circRNAs with BSJ>=2;nCircRNA_cut5 indicated number of circRNAs with BSJ>=5
Note: only circRNAs with BSJ count >= 5 were shown.Relative expression was estimated by BSJ count*100/total BSJ count in each sample
Step1: select species
Note: it may be a little slow, please be patient, we will fix it
Step2: select dataset type
Step3: select dataset
Plots
Setting
Note: it may be a little slow, please be patient, we will fix it
Note: FPB of linear RNA <0.1 was set to 0.1 and FPB of circ RNA <0.1 was set NA
loci information
loci of circRNA hotspot in all datasets
Expression of circRNA hotspot in selected dataset
Setting
Note: it may be a little slow, please be patient, we will fix it
circRNA plot
host loci information
Expression of circular RNAs
Expression of linear RNAs
Contact
Xiaosong Gu,nervegu@ntu.edu.cn
Lian Xu, xulian@ntu.edu.cn
Jian Yang, dna2009@ntu.edu.cn
Nana Jin, yongna0321@126.com
Shuqiang Zhang, sqzhang0328@ntu.edu.cn