4 — Assignment #1
This journal entry will outline my progress while completing assignment 1.
Time estimated: 7 d; taken: 8 d; date started: 2020-01-27; date completed: 2020-02-04
Dataset: GSE95573
Title of the paper:
Whole transcriptome analysis of PBMCs stimulated with either a P. aeruginosa phage PNM lysate or with its bacterial host P. aeruginosa.
Context:
Phages and phage treatments are becoming widely popular in helping to cure disorders, bacterial infections and other immune-related illnesses. A phage is essentially a virus that eats bacteria; they find and inject their DNA into specific bacteria to produce more phages. Eventually the bacteria gets filled with so much phage DNA, that it explodes and billions of phages are released to repeat the process. The image below shows a picture of a bacteriophage attached to a host bacteria.
Link: https://en.wikipedia.org/wiki/Phage_therapy#/media/File:Phage_injecting_its_genome_into_bacteria.svg
Summary of experiment:
- The experiment studies the immune responses of peripheral blood mononuclear cells (PBMCs) which are the major cells that are linked with immunity in the human body.
- The PBMCs were sampled from a healthy human donor, were stimulated for 20 h followed by lysis and RNA extraction.
- Three types of tests were performed:
- a control sample with no stimulation of phages
- a sample introducing P. aeruginosa phage PNM lysate
- and a sample with P. aeruginosa strain 573
