Bioinformatics- Assignment 8

Summary of GTEx track

Description of data:

A median of gene expression levels was taken from 52 tissues and 2 cell lines, based on RNA-seq data from the GTEx final data release in August 2019. This release was based on data from 17,382 tissue samples obtained from 948 adult post-mortem subjects.

Methods:

Tissue samples were collected using the GTEx standard operating procedures in partnership with the National Cancer Institute Biorepositories and Biospecimen. All obtained tissue samples were reviewed by pathologists in order to characterize and verify organ sources. That being said, the RNA-seq was conducted by the GTEx Laboratory, Data Analysis, and Coordinating Center. While the sequences were conducted using the STAR v2.5a assisted by the GENCODE 26 transcriptome definition. Finally, gene annotations were produced using a custom isoform collapsing procedure.

Subject and Sample Characteristics:

The donors of this study and their biospecimen were required to show no evidence of disease. Therefore, the tissue types obtained were chosen based on their clinical significance, logistical feasibility, and their relevance to the scientific goal of the project.

Expression Levels:

Were only notable in the pancreas, with a mean of approximately 12 TPM.

Summary of the GNF Atlas track

Description of data:

This track shows the investigator’s expression data from the GNF Gene Expression Atlas. The GNF Atlas contains two replicates each of 79 human tissues collected by the Affymetrix microarrays. The Affymetrix microarray assigns colors to the tissues where overexpression (red) and underexpression (green) can be detected. 

Methods:

None listed

Subject and Sample Characteristics:

None listed

Expression Class:

High expression in the gland (specific gland not specified).

Additional Questions:

1. If I wanted to search the transcriptome for an unknown sequence I would use RNA sequencing.

2 .The major difference between microarray technology and RNA sequencing is that microarray technology is used for already known genome sequencing whereas, RNA sequencing is used for discovering a new genome sequence. However, RNA sequencing can still be used for known genome sequences as well.

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