Sinem Karaman

Sinem Karaman
University of Helsinki | HY · Organotypic Vasculature Lab / Individualized Drug Therapy Research Program / RPU / Faculty of Medicine

PhD

About

59
Publications
24,763
Reads
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3,430
Citations
Additional affiliations
September 2020 - November 2021
University of Helsinki
Position
  • Principal Investigator
May 2019 - present
University of Helsinki
Position
  • Principal Investigator
November 2018 - present
University of Helsinki
Position
  • Professor (Associate)
Education
February 2018 - September 2020
Wihuri Research Institute
Field of study
  • Vascular biology
February 2016 - January 2018
Wihuri Research Institute
Field of study
  • Translational Cancer Biology
February 2015 - January 2016
ETH Zurich
Field of study
  • Pharmaceutical Sciences

Questions

Questions (4)
Question
Hi Everyone,
I would like to generate a very simple ImageJ macro, which first measures the area in a user-selected region of interest (ROI) and then the fluorescence signal intensity within the same ROI that is adjusted by manual thresholding.
Attached is a PDF, which shows the steps in the macro, ROIs are indicated with yellow selection.
As the ROI selection and the thresholding needs to be done manually in every image by the user, I would need this macro to ask the user after an image is opened:
“Select your region of interest” (=> I guess this could even be skipped by starting the macro after the manual selection of the ROI.)
And then again the macro should stop to have the user set the threshold.
Any suggestions how can I incorporate these into such a macro?
Thanks very much for any suggestions,
Sinem
Question
I would like to check in vivo insulin action, by assessing the IRS-1 and phospho-IRS-1, together with Akt and phospho Akt in adipose tissue after insulin administration. Any suggestions on protocols, and antibodies to purchase are welcome!
Question
We would like to design FRET type of probes to detect the presence of alternatively spliced isoforms of certain genes. My question is regarding the optimal probe design. How long the probe should be? Would you use pure DNA probes or would you incorporate LNAs, and if yes which part of the probe (5', middle or 3')? Does it make sense to use a probe couple like FAM - Black Hole Quencher (BHQ) 1 and TAMRA - BHQ 2 for multiplexing?
Question
I have cDNA from isolated murine macrophages (I have 4 samples from different mice) and I wanted to check the gene expression of 5 different genes. I obtained Ct values for these genes, however I am not sure how I should express these data since I am not comparing my data to any other condition (like control versus treated etc.). I thought of showing deltaCt values (difference between my target gene and my house keeping gene). Any ideas/ suggestions?

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