High Throughput Genomics
The Shomron research team focuses on the analysis of genomics aimed at understanding human disease. Combining high-throughput methods and bioinformatics, our team’s research explores gene regulators, such as microRNAs, in order to reach a global, systems perspective on the mechanistic roles small RNA play during disease development.
Among our projects: Identification of a microRNAs that are in the intersection of several oncogenes; Revealing the influence of microRNAs on pharmacogenomics and personalized medicine; Exposing pathogens in human tissues based on deep sequencing of small RNA molecules followed by subtraction and assembly of the genomes.
Overall the Shomron team pursues research that aims to deepen our understanding on the development of diseases in order to generate a significant impact through translating ideas into clinical reality.
Bioinformatics and scientific consultation
Per hour consultation for bioinformatics analysis strategy and support, in wide range of expertise from different gene expression related topics to high throughput methodologies and statistical analysis
Mutation/variant calling from DNA sequencing data
Analysis of existing whole exome/genome sequencing data to detect variants and mutations versus reference genome or paired sample and prioritization of mutations based on their predicted effects.
microRNA target gene identification
For microRNA target gene identification the lab utilizes numerous bioinformatic methods including software tools, computational methods developed in-house and integration of omic data. Downstream functional assays such as Luciferase assay are then conducted to experimentally validate the targets.
SSRI response biomarkers testing
Measuring SSRI response genes and miRNA panel on a given set of samples or computationally on a provided dataset
Network and gene ontology analysis
Network and gene ontology analysis is used for functional analysis and correlation of gene function. Relevant data integrated for all input genes or a prioritized subset of molecules and mapped onto interaction networks.
High-Throughput Sequencing of DNA/RNA, based on the Illumina Genome Analyzer IIx instrument sequencing machine.
Sample library preparation of RNA/DNA, using all current Illumina protocol
Preparation of library for sequencing from input of RNA/DNA, using all current Illumina protocol: DNA-seq, RNA-seq, small RNA, Chip-seq and de-novo assembly.
Whole exome sequencing (WES) including variant calling and prioritization.
Whole exome sequencing (WES) including variant calling and prioritization. WES is used by the lab to identify causative variants in clinical cases
Statistical analysis of TCGA data
Download, processing and query of data from The Cancer Genome Atlas (TCGA) to obtain valuable insights into the expression of various genes, genesets and miRNAs as well as mutations and comparison with clinical features.
“Wet lab” services
Wound healing assay
In-vitro assay to measure the ability of cells to migrate, adherent cells monolayers are scratched with pipette tip and allowed to close the wound for several hours and next pictured and differences between cells are analyzed.
Transwell migration and invasion assays
In-vitro assays to test the ability of cells to migrate or invade through a either transwell inserts for migration assays or Matrigel-coated invasion chambers. Following the assay cells are fixed, stained and quantified to assess the relative rate of migration/invasion
Dual luciferase reporter assay
Assay to measure transcription rate using a plasmid reporter inserted with desired sequence upstream to the Firefly Luciferase. The assay measures the Firefly and Renilla (internal control) Luciferase activities and allows to determine sequence changes on transcription. The assay could also be adapted to used 3’ UTR sequences and measure repression of transcription by microRNAs.
XTT Cell Proliferation Assay
Colorimetric method to effectively measure cell growth and drug sensitivity in cell lines. XTT is a colorless or slightly yellow compound that when reduced by Cellular Enzymes becomes brightly orange a thus allows to quantify cell number following treatment
Cloning miRNA of choice into an overexpression construct
Antagomir based blocking of a miRNA of choice
Modified real-time PCR for quantifying miRNAs
Deep Sequencing miRNA quantification
Quantifying total miRNA expression by deep sequencing includes library preparation, sequencing, raw data processing, miRNA alignment, standardization of miRNA reads and final ranking of differential miRNA expression levels
Model for HIV-1 Infection
HIV-1 infectious model of T1, Sup-T1, and H9 lymphocytes as well as HeLa-CCR5 and JLTRG-R5 cells
Intracellular FACS staining
Quantification of intracellular protein levels across various populations of cells
Transfection of miRNAs overexpression vectors to specified target cells
FOR MORE INFORMATION:
Sackler Faculty of Medicine, Room 303
Tel Aviv University, Tel Aviv 69978, Israel
E-mails: email@example.com, firstname.lastname@example.org