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This article mainly introduces what GTEx is a database, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

The full name of GTEx is as follows

Genotype-Tissue Expression

The project analyzed transcriptome sequencing and genotyping of samples from multiple combinations and organs of human body, and constructed a database of tissue-specific gene expression and regulation. The web address is as follows

Https://gtexportal.org/home/

The type of organization and the number of samples included are shown in the following figure

For all the samples, the following three kinds of analysis are carried out.

1. RNA seq

The polyA+ library was constructed by illumina Truseq kit, sequenced by Hiseq 2000 level 2500, and compared with STAR for offline data. With reference to the gtf file of gencode V19 version, the following three level were quantified.

Gene-level, using RNAseQC software to quantify the gene by raw count and TPM.

Exon-level to quantify the raw count of exon

Transcript-level, using RSEM to quantify the transcript level

2. Genotype

The sample is typed by WGS, using the process of GATK germline variants calling. The steps are as follows

Bwa-mem alignment

Picard markduplicate

BQSR

Indel realign

HaplotypeCaller

3. EQTL

Cis-eQTL analysis was carried out by FastQTL software, and the genotype was associated with gene expression.

The results of gene expression and eQTL analysis can be viewed through the official website. Taking TP53 as an example, each gene gives the following three levels of expression.

Isoform Expression

Exon Expression

Junction Expression

Corresponding to the expression of transcripts, exons and cut sequences, respectively, the expressions in different tissues are displayed in the form of a heat map, as shown below

The structure of the gene is also visualized as follows

The results of eQTL are as follows

The following two visualization methods are provided. The first is a violin drawing, eQTL violin plot, within a single organization, as shown below.

The second is used for comparisons between multiple organizations, Multi-tissue eQTL plot, as shown below

All the analysis results can be downloaded through the official website, GTEx database is not only a normal tissue gene expression database, its eQTL analysis strategy is more worthy of our reference.

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