S-STEM Scholar Alex Hames's Blog

 UCSC Genome Browser Part 3 6. a) The Repeat Masker screens DNA sequences for repeats and low complexity DNA sequences. b) SINE, LINE, LTR, DNA, Simple, Low Complexity, Satellite, RNA, Other, Unknown c) A densely shaded line represents a low number of combined base mismatch, base deletion, and base insertion associations. 10. a) LINE has the highest amount of associated repeats because it has the most amount of lighter shaded lines. b) LINE and SINE have the largest present because they have the most dense lines. c) It might be useful to see the frequency of SINES within a gene to see how well a gene might be able to be mutated or alter the expression. d) Knowing the location of microsatellites can be useful because they can be used in tracking point mutations, DNA repair, and replication errors in the gene.  e) Some assays that'll help a scientist with expression/gene regulation analysis would be PCR, CRISPR, RNA sequencing, and microarrays.

 ORegAnno in the UCSC Browser a) 1. I. Oreg #: OREG1768905 II. Region type: Transcription Factor Binding Site III. Transcription factors: MITF Ensembl - ENST00000394351 2. I. Oreg #: OREG1626239 II. Region type: Transcription Factor Binding Site III. Transcription factors: FOS Ensembl - ENST00000303562 3. I. Oreg #: OREG1939402 II. Region type: Transcription Factor Binding Site III. Transcription factors: TP53 Ensembl - ENST00000504290 b) I. Orange  II. It is important to know the regulatory elements in a gene because those elements regulate what parts of the DNA are replicated and how the gene/DNA might be manipulated to make a certain protein.  c) I think the first assignment was the most interesting to me because I was able to choose my proteins among 26 other ones, and find a lot of information about a new protein I had never heard of. I thought it was fascinating to dive into and learn about this new protein and new world that is database research. Some potentia...

 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...

 UCSC Genome Browser Gene: SLC5A1  Chromosome and position: chr22:32,043,261-32,113,029- 69,769 bp When NCBI RefSeq is put to full in the "Genes and Gene Predictions" section, the gene is mapped out and shows the introns associated with the gene.  When you click the track heading, you condense the newly added RefSeq track and similar subtracks. Clicking on the gene name sends you to an information page about the gene where you can find a summary of the gene, description, data displays, and methods of review for the data.  Browser image: