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Basic Laboratory Work in Life Science Experiments

In this lecture, we will perform bioinformatics experiments such as “Sequencing”, “Biochemical Reaction Simulation”, and “Gene Expression Profiling” (← Our Lab is in charge of this). This lecture is for students in , department of Bioinformatics and Systems Biology or department of Biophysics and Biochemistry.

Please refer to Lecture’s Wiki or Repository’s Wiki to check the schedule.

Wet Experiment (MicroArray)

digraph WetExperimentOverviewGraph { graph [ charset = "UTF-8"; label = "Wet Experiment", labelloc = "t", labeljust = "c", bgcolor = "#1f441e", fontcolor = "white", fontsize = 26, fontname = "times", style = "filled", rankdir = TB, margin = 0.2, ranksep = 1.0, nodesep = 0.9, layout = "dot", compound = true, ]; node [ shape = note, style = "solid,filled", fontsize = 20, fontcolor = 6, fontname = "fantasy", color = "#5f939a", fillcolor = "#cdf0ea", fixedsize = false, margin = "0.2,0.2", ]; tissue_samples [label="HeLa cell"] tissue_sample_mock [fillcolor="white" label="HeLa cell\n(mock)"] tissue_sample_siVIM [fillcolor="white" label="HeLa cell\n(+siVIM-270)"] tissue_sample_siVIM_XXX [fillcolor="white" label="HeLa cell\n(+siVIM-270-2'OMe)"] mRNA_molecules [label="mRNA molecules"] labeled_cDNA_molecules [label="Labeled cDNA molecules"] DNA_microarray [label="DNA microarray"] edge [ style = solid, fontsize = 16, fontname = "times", fontcolor = white, color = white, labelfloat = false, arrowhead = vee, headport = n, arrowsize = 1.5, ]; tissue_samples -> tissue_sample_mock; tissue_samples -> tissue_sample_siVIM_XXX; tissue_samples -> tissue_sample_siVIM [label="Transfection"] tissue_sample_siVIM -> mRNA_molecules [label="Isolate mRNA"] mRNA_molecules -> labeled_cDNA_molecules [label="Make cDNA by reverse transcription,\nusing fluorescently labeled nucleotides."] labeled_cDNA_molecules -> DNA_microarray [label="Apply the cDNA mixture to a microarray,\na micro-scope slide on which copies of single-stranded DNA fragments\nfrom the organism's genes are fixed, a different gene in each spot.\nThe cDNA hybridizes with any complementary DNA on the microarray."] }

Package

You can install this package with the following command etc.

$ pip install "git+https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments.git"

This package is for facilitating the lecture, so it contains many utility functions, such as data handling and anonymous questions.

However, it also contains functions to easily plot MAplot and XYplot . If you want to know how to use those plotting functions, please refer to the followings.

module

Notebook

documentation

plotly

notebook/Local/Main-Lecture-Material-plotly.ipynb

teilab.plot.plotly module

matplotlib

notebook/Local/Main-Lecture-Material-matplotlib.ipynb

teilab.plot.matplotlib module

Installation

I recommend you to use Pyenv and Poetry to set up the required environment.

$ git clone https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments.git
$ cd TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments
$ pyenv install 3.8.9
$ pyenv local 3.8.9
$ python -V
Python 3.8.9
$ poetry install

If you want to use Jupyter Notebook with this environment, check this notebook.

Indices and tables