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This article will explain in detail how to use the exoRBase database for everyone. Xiaobian thinks it is quite practical, so share it with you for reference. I hope you can gain something after reading this article.

Exosomes, translated as exosomes, are vesicles secreted by cells with a diameter of 30-150nm. They belong to extracellular vesicles and contain different kinds of RNA. They can regulate the behavior of receptor cells and can be used as circulating biomarkers of diseases. They are widely found in blood, saliva, urine and other body fluids.

exoRBase is a database of RNA in human blood exosomes.

http://www.exorbase.org/

Transcriptome sequencing data for blood exosomes were collected from the GEO database. A total of 87 samples from 6 experiments were collected. The sample types of each experiment were different.

normal persons(NP)

coronary heart disease(CHD)

colorectal cancer(CRC)

hepatocellular carcinoma(HCC)

pancreatic adenocarcinoma(PAAD)

breast cancer(BC)

In addition, 5 human whole blood samples were supplemented, and the number of different types of samples was summarized as follows

For the data of these 92 samples, RNA was analyzed using the pipeline shown below

For the raw data of sequencing, adapter and low-quality sequences were removed by trimomatic software, clean reads were aligned with hg38 genome by hisat2, mRNA and lncRNA were quantified by featurecounts software, and expression was normalized by TPM.

For circRNA, ACFs and find_circ software were used to predict simultaneously, and the intersection of the two results was taken as the final result. RPM was used to normalize the expression quantity during quantification.

On the basis of the above analysis results, some RNA data were newly added by searching exosomal RNA related literatures in pubmed database. The number of RNA from all sources is summarized as follows

For mRNA and lncRNA, tissue-specificity was calculated by combining expression profile data from different tissues in the GTEx project.

Through the Browse menu in the navigation bar, you can view various RNA information in exosomes, as shown below.

Through the Search menu of the navigation bar, you can conveniently retrieve the database, as shown below.

The database is aimed at RNA in exosomes, and its construction idea is worth learning from.

About "how to use exoRBase database" this article is shared here, I hope the above content can be of some help to everyone, so that you can learn more knowledge, if you think the article is good, please share it to let more people see.

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