HAMES_DBI.A9

 UCSC Genome Browser Part 2

6. I. Description of the data: The NIH Genotype-Tissue Expression project is used to study genetic  variation and gene expression in human tissues. The track shows median gene expression in 52 tissues and 2 cell lines based on data from 17,382 tissues obtained from 948 post-mortem adults.

II. Tissue samples were obtained using the GTEx operating procedures of tissue collection and specimens were reviewd by pathologists to verify the organ source. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize the specimens. The RNA-seq was performed by GTEx and were aligned to the human genome using STAR v2.5.3a assisted by the GENCODE 26 transcriptome defintion. Gene annotations were produced using a custome isoform collapsing procedure that excluded and then included extrons/introns. Gene expression levels were called via the RNA-SeQC tool after filtering it by unique mapping, proper pairing, and exon overlap. 

III. The goal of GTEx required the donating specimen tissue had no evidence of disease; the tissue types were collected based on their clinical significance, logical feasibility, and relevance to GTEx's goal.

IV. 

7. a) I. The GNF Gene Expression Atlas track contains two replicates each of 79 human tissues run over Affymetrix microarrays. The averages of the related tissues are shown in the track data. 
II. There are no Methods displayed.
III. There are no Subject and Sample Characteristics displayed.
IV. 
b) I. RNA sequencing
II. The main difference between RNA and Affymetrix microarrays is the specificity of the data as well as how it is presented. RNA sequencing is a lot more specific by extracting data of tissue for specific parts of the body, while microarrays are a lot more general in what tissue they record data for. Also, RNA sequencing is presented as a bar graph while microarrays are presented with a color scale key. 




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