CHEN MORDECHAY 203215454 Supervisors Professor Eitan Bachmat Doctor Alal Eran Traditional brain research is biased Psychiatric drugs are being tested on humans We wish to test drugs in a safe lab environment ID: 780099
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TRANSCRIPTOMIC CHARACTERIZATION OF INDUCED NEURONS
CHEN MORDECHAY203215454Supervisors:Professor Eitan BachmatDoctor Alal Eran
Slide2Traditional brain research is biased
Psychiatric drugs are being tested on humans – We wish to test drugs in a safe lab environmentWe wish to examine the use of Induced Pluripotent Stem Cells in researching brain diseasesTHE PROBLEM
Slide350,000 continuous features for each sample
Each feature represents a different geneWe measure the expression levels of each gene in each individualTranscriptomic Characterization
Slide4THE COMPLETE RNAseq PIPELINE
Slide5ANALYTIC FRAMEWORK
DATA PREPROCESSINGGather expression matrices
Gather annotations for our samples
2) FEATURE SELECTION
PCA
T-SNE
Differentially expressed genes selection
3) CLASSIFICATION SCHEMES
K-Means
Hierarchical Clustering
Linear Model
4) RESULTS GENERATION
Visualizations
Reports
Slide6INTERACTIVE RESEARCH INTERFACE
Written in R using Shiny, Hosted on the cloudProcessing of datasets is accomplished using BGU HPC
Slide7RESULTS
What we have discovered…
Slide8Positive Control
Dataset source: GTEx - Publicly available250 Samples10 tissues25 samples of each tissueTissues
Adipose Tissue
Blood
Brain
Breast
Colon
Heart
Muscle
Ovary
Pancreas
Testis
Slide9Results - Positive Control
Slide10Treatment Response
Private Dataset from a drug discovery company30 samplesDisease: Rett SyndromeGenome editedPharmacologically treated
Treatment control
Slide11Results – Treatment Response
Slide12Summary: What we’ve accomplished
Distributed RNAseq processing pipelineSemi-Supervised flexible classification framework developmentImplementation via a cloud based research platform
Slide13Special thanks is given to Einat Shusterman and Ido Shalev for their invaluable contribution to the project!
Slide14TRANSCRIPTOMIC CHARACTERIZATION OF INDUCED NEURONS
CHEN MORDECHAY
203215454
Supervisors:
Professor Eitan
Bachmat
Doctor
Alal
Eran