Internship report

    UNIST UNDERGRADUATE SCHOOL

     School of Life Science

 

 

RESEARCH INTERNSHIP REPORT

 

 

 

Student:      ___20132023____    ___Madina           _  Seidualy____

                  Student ID                 First name                  Last name

 

Track:      ____BIO ___ _     _____BME_ ___          Grade:  __Senior ___

                1 Track               2 Track

 

Advisor:   ____SLS_ ___ __    ___Jong Hwa_____    ____Bhak ____

                School                    First name                   Last name

 

 

Starting Date:     12/26/2016 (mm/dd/yyyy)

Ending Date:   02/20/2017 (mm/dd/yyyy)

 

 

 

 

 

• The Genomic Lab

  The Genomics lab was established in July 2014 by a group of researchers in Korea.

The genomics lab is a team of dedicated people who want to understand the structure and function of the genomes on Earth. The main application area is anti-cancer and anti-aging. The topics are unlimited. TGL belongs to BME (Biomedical Engineeing department of UNIST) in SLS (School of Life Science).

Professor Bhak Jong Hwa is a director of the The genomic Institute in the UNIST. I had a chance to get an experience in this lab for two months. The Genomic Institute run diverse projects like whole genome sequencing, transcriptome analysis and etc..

 Currently, TGI doing genome sequencing analysis of whale shark, coral genome and jellyfish. Moreover, TGI is not confined on sequencing of the living species, either do relevance projects concerning problems in society, and trying to identify some genetic markers for those characteristic issues.

 

 

 

• Performance in the Lab

Time	Tasks	Accomplishment
1st Week	Introduction to Lab, learning general tools, introduction to genomic databases	I’ve learned basic multiple alignment programs, and compute protein alignments. I’ve constructed phylogenetic tree and studied about genome browsers.
2nd Week	Literature search about candidate genes of the Whale shark	By using information from genome browsers (DAVID, Ensembl, NCBI, Unipot) have collected data about positively selected genes of Whale Shark. I’ve found out fascinating facts about whale shark through protein analysis.
3rd Week	Literature search about candidate genes of the Whale shark	Close search about HP1BP3, and did multiple sequence alignments via MEGA7. I’ve recognized W2 domain gain in HP1BP3 through InterPro database.
4th Week	Introduction to Bioinformatics, learning Perl	I’ve introduced to Linux Terminal, and started study on Perl.
5th Week	Perl coding, constructing HeatMap using R	Doing simple calculations in DNA, protein data in terminal through by writing my own coding scripts. Learned and build HeatMap in R studio.
6th Week	Calculation of the length of each scaffolds with certain gene in it from whale shark genome data.	Through tasks improved coding skills, and got used to genomic data. I’ve started using BioPerl.
7th Week	Mapping paired end reads to the reference genome of the Whale Shark	Study on DNA sequencing processes. In order to sequence alignment against a large reference genome learned about BWA and corresponding steps.
8th Week	Learning about various integrative analyses for multi omics data	Read paper about “Integrated Genomic Characterization of Papillary Thyroid Carcinoma”. I’ve learned about Circos program and other tool for integrating genomic data.

 

 

 

 

 

 

 

 

 

• Self-Evaluation

 During the two month of internship in The Genomic Institute I’ve learned important values of the genomics. Before doing internship, I had known diverse things and learned plenty of stuffs in research area but I had had difficulties in correlating them. All seemed to me complicated. However, after having internship experience, I organized every research step in sequential order, and I could make whole picture of it. Now I know well how genome analysis have done. As an example, in below table I provided brief summary of the main genomic analysis I’ve learned so far:

STEPS	EXPLANATION	FORMATS&TOOLS
Raw Data	From Illumina sequencing	.bcl format  (base cells per cycle)
Demultiplexing	Changing format from .bcl -> fastq	.fastq (+quality scores)
Downstream alignment	Sequence alignment to reference genome or creating de novo assembly.	Fastq->SAM  Sam ->bam (univercal file format for mapped seq. reads) BWA, SOAPdenovo
Variant Calling	find SNP,SNV,INDELS	SAMtools, GATK
Visualization of DATA	Integrative genomic viewer, UCSC Genome browser	Circos,Heatmap,etc

  

In above table, in each step there are plenty of tools used for, which I have to learn in detail in near future.

 In addition, I’ve acknowledged that Bioinformatics is the main tool in genomic analysis. I cannot imagine how would researches in big mass of information of the DNA and protein would computed without programming codes. I have strong desire to fortify my bioinformatics skill further in order to do rewarding researches, and correctly interpret biological data.

 Since DNA carries all genetic instructions used in growth, development, functioning and reproduction of all living organisms, fascinating thing is that, while conducting researches in genomic lab you learn, work and know about everything every day. Compare to laboratories, where researches are confined in specific topic Genomic department researchers observe everything and create big pictures of the life. For a student like me who has big passion in learning about living organisms it was best experiences.