S-Stem Scholar Anthony Luna's Blog

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 diseas...

Assignment 8 had me get acquainted with the UCSC genome browser, which is saturated with all different kinds of genomic information. I looked up my protein AMY1B and explored its genetic sequence along with some other loci on the same chromosome. That being said, when I filtered what was displayed in the data track to "NCBI RefSeq" my data track shrunk significantly, only displaying one gene body. When I clicked on the gene body it took me to a new window that listed the specifics of the gene that I had already read about in previous databases used. Taking note of this, it showed me how meticulous these databases strive to be in putting out information. Below is the best image I could get of the initial data track displayed in the UCSC genome browser.