Services and produced provided by RegBio Lab @Yeditepe University

Flow cytometric analysis

Picture
Flow cytometry (Beckman Cytoflex S)
Equipped with 4 lasers (including UV) and plate loader for automated loading, post-compensation
Flow cytometry related publications:,
  1. Fatih Kocabas(co-first author), et al. "The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche." Cell Stem Cell 7, no. 3 (2010): 380-390. [Impact Factor: 25.421]
  2. Fatih Kocabas, et al. "Meis1 regulates the metabolic phenotype and oxidant defense of hematopoietic stem cells." Blood (2012). [Impact Factor: 9.898]
  3. Fatih Kocabas, et al. "The Hypoxic Epicardial and Subepicardial Microenvironment." Journal of Cardiovascular Translational Research (2012): 1-12.   [Impact Factor: 3.062]
  4. Fatih Kocabas, et al. "Metabolic Characterization of Hematopoietic Stem Cells." In Hematopoietic Stem Cell Protocols, pp. 155-164. Springer New York, 2014. 
  5. Lamia Yazgı Alyazıcı, Dolay Damla Çelik, Esra Albayrak, Merve Aksöz, Fatih Kocabaş. Küçük moleküllerle mezenkimal kök hücre proliferasyonunun indüklenmesi. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  6. Seyma Yildirim, Serdar Sezer, Zeynep Kocer, Fatih Kocabas, et al .Cartilage Regeneration of Human Adipose-derived Mesenchymal Stem Cells on Novel Chitosan- Based Hydrogel Scaffold.2nd International Stem Cell Congress. Antalya. 15-18 Oct 2015. 

More available here: ​
​
Flow cytometry analysis (tube or 96 plate format)

Specific applications / services available:
  1. Human HSC analysis (CD34, CD90, CD133) 
  2. ​Mouse HSC analysis (LSKCD34low, LSKCD150)
  3. AD-MSC flowcytometric characterization (CD...)
  4. BM-MSC flowcytometric characterization (CD...)
  5. Apoptosis analysis (Annexin V-PI)
  6. Cell cycle analysis (Ho-Pyronin Y)
  7. 242 human cell surface markers Human CD panel (BD lyoplate All CD panel) 
​
Staining and analysis protocols: 
​
For other inquiries please contact to PI

Bioactivity analysis

Picture
Multimode reader (ThermoFisher, Varioscan Lux, full version) 
Equipped with absorbance, monochromator fluorescence (all wavelengths), luminescence (with injector), and plate loader for automated loading
Activity analysis related publications:,
  1. Fatih Kocabas, et al. "Fluorometric RdRp assay with self-priming RNA." Virus Genes (2015): 1-7. PDF 
  2. Fatih Kocabas*, and Galip S. Aslan. "Fluorometric CCHFV OTU protease assay with potent inhibitors." Virus genes (2015): 1-8. PDF 
  3. Fatih Kocabas, et al. "Metabolic Characterization of Hematopoietic Stem Cells." In Hematopoietic Stem Cell Protocols, pp. 155-164. Springer New York, 2014. 
  4. Fatih Kocabas, et al. "Hypoxic metabolism in human hematopoietic stem cells." Cell & Bioscience 5, no. 1 (2015): 39 [Impact Factor: 3.63] PDF​
  5. Ali O Boztas, Ozgur Karakuzu, Gabriela Galante, Zafer Ugur, Fatih Kocabas, et al. Synergistic Interaction of Paclitaxel and Curcumin with Cyclodextrin Polymer Complexation in Human Cancer Cells. Molecular Pharmaceutics (June 3, 2013). DOI: 10.1021/mp400101k [Impact Factor 4.782] 
  6. Galip Servet Aslan, Fatih Kocabas. Development of fluorometric CCHFV OTU protease assay and identification of potent inhibitors. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul. 
  7. Pınar Siyah, Fatih Kocabaş. Hücresel İmmünitenin Baskılanmasında Rol Alan Putatif Malarya OTU Deübikütinazlarının Modellenmesi ve İnhibitör Taranması. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  8. Fatih Kocabaş. Rekombinant KKKAV OTU proteazının üretimi ve inhibitörlerin geliştirilmesi. 11. Ulusal Afinite Teknikleri Kongresi. 15-17 June, 2017. Kuşadası, Aydın, Turkey


More available here: ​
Multimode reader activity analysis (96 and 384 well plate format)

Specific applications / services available:
  1. MTS analysis (cell viability and proliferation analysis)
  2. WST1 analysis (cell viability and proliferation analysis)
  3. LDH analysis (cell viability and proliferation analysis)
  4. ATP assay (ATP content analysis, metabolic characterization of cells, cell viability and proliferation analysis)
  5. Activity analysis of small molecules in a panel of cancer cell lines 
  6. Luc reporter assays (Promega Dual Luciferase Assays)
  7. OTU protease enzymatic fluorescence activity analysis
  8. Fluorometric RdRp assay with self-priming RNA (if kit is provided)
  9. All enzymatic assays (if kit is provided)

Activity analysis protocols: 

For other inquiries please contact to PI

Protein expression and purification

Picture
Acta prime (GE Healthcare) FPLS Protein Purification System
Equipped with Histag columns (1-5 mL) 
Protein expression and purification related publications:,
  1. Fatih Kocabas, and Galip S. Aslan. "Fluorometric CCHFV OTU protease assay with potent inhibitors." Virus genes (2015): 1-8. PDF 
  2. Fatih Kocabas, et al. "Fluorometric RdRp assay with self-priming RNA." Virus Genes (2015): 1-7. PDF 
  3. Semih Arbatlı, Merve Uslu, Pinar Siyah, Fatih Kocabas. Production of recombinant CAS9 protein and examination of Cas9 destabilizer molecules.CRISPR: From Biology to Technology and Novel Therapeutics. 22-24 October 2017, Sitges – Spain (http://cell-symposia.com/crispr-2017/)
  4. Merve Uslu, Semih Arbatlı, Pınar Siyah, Fatih Kocabaş. Rekombinat CAS9 proteini üretimi ve Cas9 destabilizör moleküllerin araştırılması. 11. Ulusal Afinite Teknikleri Kongresi. 15-17 June, 2017. Kuşadası, Aydın, Turkey
  5. Pınar Siyah, Fatih Kocabaş. Putatif Malarya OTU Proteinlerinin Karakterizasyonu ve İnhibitör Taramaları. 11. Ulusal Afinite Teknikleri Kongresi. 15-17 June, 2017. Kuşadası, Aydın, Turkey
  6. Fatih Kocabaş. Rekombinant KKKAV OTU proteazının üretimi ve inhibitörlerin geliştirilmesi. 11. Ulusal Afinite Teknikleri Kongresi. 15-17 June, 2017. Kuşadası, Aydın, Turkey
  7. Semih Arbatlı, Merve Uslu, Pınar Siyah, Fatih Kocabaş. Gen düzenlemede istenmeyen hedef dışı kırılmaları engelleyici Cas9 destabilizör moleküllerin geliştirilmesi. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  8. Pınar Siyah, Fatih Kocabaş. Putatif Malarya OTU Proteinlerinin Karakterizasyonu ve İnhibitör Taramaları. 11. Ulusal Afinite Teknikleri Kongresi. 15-17 June, 2017. Kuşadası, Aydın, Turkey
  9. Pınar Siyah, Fatih Kocabaş. Hücresel İmmünitenin Baskılanmasında Rol Alan Putatif Malarya OTU Deübikütinazlarının Modellenmesi ve İnhibitör Taranması. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  10. Galip Servet Aslan, Fatih Kocabas. Development of fluorometric CCHFV OTU protease assay and identification of potent inhibitors. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul. 
More available here: ​
Protein expression in bacteria and HisTag purification

Specific applications / services available:
  1. ​HisTagged OTU protease protein
  2. HisTagged spCAS9 protease protein 
  3. Cloning and expression of proteins with HisTag (Includes gene synthesis, Histag addition, expression in 4 different bacterial strains, and purification with Acta prime system)
Protein expression and purification protocols: 
​
For other inquiries please contact to PI

In silico drug screening

Picture
Compecta Super Computer (Ubuntu)
Equipped with 42 CPUs
upto ​100.000 small molecules / day
In silico drug screening related publications:,
  1. Fatih Kocabas, Enes K. Ergin. Identification of small molecule binding pocket for inhibition of Crimean-Congo hemorrhagic fever virus OTU protease. TJB. DOI: 10.3906/biy-1501-56 
  2. Fatih Kocabas, and Galip S. Aslan. "Fluorometric CCHFV OTU protease assay with potent inhibitors." Virus genes (2015): 1-8. PDF 
  3. Semih Arbatlı, Merve Uslu, Pınar Siyah, Fatih Kocabaş. Gen düzenlemede istenmeyen hedef dışı kırılmaları engelleyici Cas9 destabilizör moleküllerin geliştirilmesi. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  4. Pınar Siyah, Fatih Kocabaş. Hücresel İmmünitenin Baskılanmasında Rol Alan Putatif Malarya OTU Deübikütinazlarının Modellenmesi ve İnhibitör Taranması. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
  5. Raife Dilek Turan, Enes K. Ergin, Fatih Kocabas. The Establishment of Homeobox Family Inhibitor Library and Meis1 Reporter Assays. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul.
  6. Galip Servet Aslan, Fatih Kocabas. Identification of small molecule binding pocket and potent inhibitors of CCHFV OTU deubiquitinase. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul.
  7. Galip Servet Aslan, Fatih Kocabas. Development of fluorometric CCHFV OTU protease assay and identification of potent inhibitors. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul. 

More available ​here: ​
In silico drug screening based on AutodockVina and Padel ADV

Specific applications / services available
  1. Assembly of library of small molecules for target of interest
  2. Protein preperation and grid box generation (AutoDock Vina platform)
  3. Performing in silico screening (AutodockVina, PadelADV system, upto 100.000 small molecules /day)

In silico protocols and platforms: 

For other inquiries please contact to PI
​

Gene editing and gene targeting services

Picture
Gene editing and target validation services
Gene editing and gene targeting related publications:,
  1. Semih Arbatlı, Merve Uslu, Pinar Siyah, Fatih Kocabas. Production of recombinant CAS9 protein and examination of Cas9 destabilizer molecules.CRISPR: From Biology to Technology and Novel Therapeutics. 22-24 October 2017, Sitges – Spain (http://cell-symposia.com/crispr-2017/)
  2. Batuhan Kalkan, Fatih Kocabas. Development of TYR Gene Editing Technologies for Vitiligo Disease.CRISPR: From Biology to Technology and Novel Therapeutics. 22-24 October 2017, Sitges – Spain (http://cell-symposia.com/crispr-2017/)
  3. Merve Uslu, Sefa Aydin, Jun Ke Zheng, Fatih Kocabaş. Development of HematoMiR technologies for the hematopoietic stem cells expansion with enhanced DNA repair function. Cell Symposia. CRISPR: From Biology to Technology and Novel Therapeutics. 22-24 October 2017, Sitges – Spain (http://cell-symposia.com/crispr-2017/)
  4. Semih Arbatlı, Merve Uslu, Pınar Siyah, Fatih Kocabaş. Gen düzenlemede istenmeyen hedef dışı kırılmaları engelleyici Cas9 destabilizör moleküllerin geliştirilmesi. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey​
  5. Batuhan Mert Kalkan, Etkin Parlar, Fatih Kocabaş. Vitiligo hastalığının tedavisinde gen düzenleme teknolojilerinin geliştirilmesi. XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey

More available ​here: ​
Gene editing and gene targeting services

Specific applications / services available
  1. gRNA cloning into LentiCrispr2
  2. gRNA target verification (colony selection, DNA isolation target primer desingand Sanger sequencing)
  3. Histagged CAS9 protein production
  4. in vitro gRNA transcription
  5. RNP complex (
  6. Histagged CAS9 protein & in vitro transcribed gRNA)
  7. Repair template cloning (with GPF)

Gene editing and gene targeting protocols: 

For other inquiries please contact to PI
​

MEIS inhibitors ( MEISi-1 and MEISi-2 )

Picture
MEIS inhibitors developed by Prof Kocabas affectively inhibit MEIS activity in vitro and in vivo. We have developed two small molecule MEIS inhibitors named MEISi-1 and MEISi-2.
MEIS and MEISi related publications and talks​
  1. Fatih Kocabas (co-first author), Ahmed I Mahmoud, Shalini A. Muralidhar, Wataru Kimura, Ahmed S. Koura, Suwannee Thet, Enzo R. Porrello, and Hesham A. Sadek. Meis1 regulates postnatal cardiomyocyte cell cycle arrest. Nature 497, no. 7448 (2013): 249-253. [Nature Impact Factor: 42.351] PDF
  2. Fatih Kocabas, Junke Zheng, Suwannee Thet, Neal G. Copeland, Nancy A. Jenkins, Ralph J. DeBerardinis, Chengcheng Zhang, and Hesham A. Sadek. "Meis1 regulates the metabolic phenotype and oxidant defense of hematopoietic stem cells." Blood (2012). [Blood Impact Factor: 9.898] PDF
  3. Fatih Kocabas(co-first author), Tugba Simsek, Junke Zheng, Ralph J. DeBerardinis, Ahmed I. Mahmoud, Eric N. Olson, Jay W. Schneider, Cheng Cheng Zhang, and Hesham A. Sadek. "The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche." Cell Stem Cell 7, no. 3 (2010): 380-390. [Cell Stem Cell Impact Factor: 25.421] PDF
  4. Merve Aksoz, Raife Dilek Turan, Esra Albayrak, Fatih Kocabaş*. Emerging Roles of Meis1 in Cardiac Regeneration, Stem Cells, and Cancer. Current drug targets. 2017 Jul 24. doi: 10.2174/1389450118666170724165514 Full text
  5. Fatih Kocabas*. Emerging Roles of MEIS1 in Hematopoiesis and Heart Regeneration. ISBN 978-3-659-59658-2. LAP LAMBERT Academic Publishing, Germany. February 23, 2015. Link
  6. Fatih Kocabas*. MEIS1: At the Crossroads between Metabolic and Cell Cycle Regulation. PhD diss., 2013. UT Southwestern Electronic Theses and Dissertations. PDF​
  7. Şeyma Nur Eren, Raife Dilek Turan, Fatih Kocabaş. Hücre ekspansiyonunda etkin MEIS inhibitorlerinin geliştirilmesi.  Hücresel İmmunoterapi sempozyumu. 20-22 October 2017. Trabzon, Turkey
  8. Semih Arbatlı, Raife Dilek Turan, Galip Servet Aslan, Esra Albayrak, Serdar Durdağı, Fatih Kocabaş. Identification of Cardiogenic and Hematopoietic MEIS Inhibitors that Enhance Cellular Proliferation and HDR Gene Expression. 5th International Bau Drug Design Congress. 19-21 October, 2017. Istanbul, Turkey
  9. Semih Arbatlı, Merve Uslu, Fatih Kocabaş. Identification of Cas9 small molecule inhibitors.Identification of Cardiogenic and Hematopoietic MEIS Inhibitors that Enhance Cellular Proliferation and HDR Gene Expression. 5th International Bau Drug Design Congress. 19-21 October, 2017. Istanbul, Turkey
  10. Fatih Kocabaş, Semih Arbatlı, Raife Dilek Turan, Galip Servet Aslan, Esra Albayrak, Merve Uslu, Serdar Durdağı, Zafer Gülbaş. Identification of Hematopoietic and Cardiogenic MEIS Inhibitors that Enhance Cellular Proliferation and HDR Gene Expression. 5th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon’17). 8-10 September 2017. Istanbul, Turkey
  11. Raife Dilek Turan, Enes K. Ergin, Fatih Kocabas. The Establishment of Homeobox Family Inhibitor Library and Meis1 Reporter Assays. 3rd International BAU Drug Design Congress. Oct 1-3. 2015. Istanbul.
  12. Fatih Kocabas, Ahmed I Mahmoud, Shalini Muralidhar, Suwannee Thet, Enzo R. Porrello, Eric Olson, and Hesham A. Sadek. Meis1 is a key regulator of post-natal cardiomyocyte cell cycle arrest. Basic Cardiovascular Sciences 2012 Scientific Sessions, New Orleans, Louisiana, USA (July 23-26, 2012). Circulation Research. 111(4_MeetingAbstracts) Supplement 1, July 20, 2012. [Award winning Abstract] [Circulation Research Impact Factor: 9.489] 

More available ​here: ​

Emerging roles of MEIS

Patents and related publications
  1. Fatih Kocabas. MEİS proteinlerini inhibe eden bir kombinasyon. ÜSİMP Ulusal Patent Fuarı 2017. 6-7 N
  2. Ulusal Patent: 2016/16602 sayılı, "MEIS PROTEİNLERİNİ İNHİBE EDEN BİR KOMBİNASYON"
  3. PCT 25418.57 nolu, PCT/TR2017/050445 sayılı "MEIS PROTEİNLERİNİ İNHİBE EDEN BİR KOMBİNASYON"
Awards, funds and related publications
  1. Poster Award. Fatih Kocabas, Ahmed I Mahmoud, Shalini Muralidhar, Suwannee Thet, Enzo R. Porrello, Eric Olson, and Hesham A. Sadek. Meis1 is a key regulator of post-natal cardiomyocyte cell cycle arrest. Basic Cardiovascular Sciences 2012 Scientific Sessions, New Orleans, Louisiana, USA (July 23-26, 2012). Circulation Research. 111(4_MeetingAbstracts) Supplement 1, July 20, 2012. [Award winning Abstract] [Circulation Research Impact Factor: 9.489] 
  2. Oral Presentation Award. Biruni University, Computer Aided Drug Design Meeting. May 2016. 
  3. Best poster award. October 2015. 2nd International Congress of Stem Cell and Cellular Therapies. Antalya
  4. Oral Presentation Award. MEMBS 2015 Congress awarded Dr. Kocabas for his talk titled "Small Molecule Induced Hematopoietic Stem Cell Expansion". 
  5. Funding: TUBITAK ARDEB 3501 Career Development. 2016-2018. Identification of Cardiogenic Meis1 Inhibitors
  6. ​Funding: Turkish Society of Hematology (Türk Hematoloji Derneği) Research Award. 2016-2017. Ex vivo Hematopoietik Kök Hücre  (HKH) çoğaltılmasında etkili Meis1 inhibitörlerinin araştırılması.
For inquiries of MEISi-1 and MEISi-2 please contact to PI. We have limited quantities at the moment, 1mg-10 mg packages are available, 
​

Automated fluorescence imaging platform

Picture
Automated imaging platform
Cytell Cell Imaging System
Automated imaging related publications and talks
  1. Merve Uslu, Sefa Aydin, Jun Ke Zheng, Fatih Kocabaş. Development of HematoMiR technologies for the hematopoietic stem cells expansion with enhanced DNA repair function. Cell Symposia. CRISPR: From Biology to Technology and Novel Therapeutics. 22-24 October 2017, Sitges – Spain (http://cell-symposia.com/crispr-2017/)
  2. Semih Arbatlı, Raife Dilek Turan, Galip Servet Aslan, Esra Albayrak, Serdar Durdağı, Fatih Kocabaş. Identification of Cardiogenic and Hematopoietic MEIS Inhibitors that Enhance Cellular Proliferation and HDR Gene Expression. 5th International Bau Drug Design Congress. 19-21 October, 2017. Istanbul, Turkey
  3. Fatih Kocabaş. Hematopoetik kök hücre ekspansiyon teknolojilerinin geliştirilmesi. Yildiz Teknik Universitesi.  April, 2017. İstanbul, Turkey
  4. Galip Servet Aslan, Esra Albayrak, Raife Dilek Turan, Emre Can Tüysüz, Serli Canikyan, Neslihan Meriç, Zafer Gülbaş, Fikrettin Şahin, Fatih Kocabaş. Epigenetik manipülasyonların ex vivo hematopoetik kök hücre çoğaltımına etkileri . XXIV. Ulusal İmmünoloji Kongresi. 27 – 30 April 2017, Istanbul – Turkey
More available ​here: ​
Automated fluorescence imaging system

1- Total imaging and cell counting of 96-well plate wells (DAPI or Ho stained cells)
2-Cell cycle analysis by microscopy (refer to manufactures protocols)
3-Autofocused and autocollection of images for upto 4-5 modes (Blue, Green, Red, Far Red, Bright microscopy modes)

For inquiries please contact to PI
​

TÜBİTAK project consultancy and writing

We have experience (accepted proposals) for the following but not limited to: 
TÜBİTAK ARDEB 1001 projects consultancy and writing
TÜBİTAK ARDEB 1002 projects consultancy and writing​
TÜBİTAK ARDEB 1003 projects consultancy and writing​
TÜBİTAK ARDEB 3501 projects consultancy and writing​
TÜBİTAK BİDEB 2232 projects consultancy and writing​
TÜBİTAK BİDEB 2236 projects consultancy and writing​
TÜBİTAK BİDEB 2216 projects consultancy and writing​
For inquiries please contact to PI
​

Other services

Yeditepe Üniversitesi Rejeneratif Biyoloji Laboratuvarı Tarafından Sunulan Servisler

  1. Hematopoietik Kök Hücre Analizi: Murine hematopoetik kök hücrelerin miktarı akış sitometrisi ile analizi gerçekleştirilmektedir. LSKCD34low, Lin-, Sca-1+, c-Kit+, CD34Low fare markerlerinin analizi gerçekleştirilir. İnsan kan kök hücrelerinin analizi CD34, CD133, CD90 karakterizasyonu gerceklestirilebilmektedir. Kemik iliği ve kandan analizler gerçekleştirilmektedir. 100 uL’lik reaksiyonlar analiz başına ücretlendirilir.
  2. Hematopoetik Hücrelerin Magnetik Separasyonu : BD IMagnet ile murine lineage negatif popülasyonun separasyonu gerçekleştirilmektedir. Bu deplesyonda Anti-mouse CD3e, clone 145-2C11 Anti-mouse CD11, clone M1/70, Anti-mouse CD45R/B220, clone RA3-6B2, Anti-mouse Ly-6G and Ly-6C (Gr-1), clone RB6-8C5, Anti-mouse TER-119/Erythroid Cells, clone TER-119 kullanilmaktadir.
  3. Kalp dokusundan kardiyak dijesyon sistemi ile kardiyak hücrelerinin eldesi: Fare, Rat ve Tavsan kalbinden kardiyak hücrelerin izolasyonu gerçekleştirilir. Bu hayvanların prosedür öncesinde anestesize edilip kardiyak dijesyon sistemine  kalplerinin nakledilmesi gerekmektedir.
  4. Neonatal kardiyomiyosit eldesi ve kültürü: Rat ve kanatlı neoanatal kardiyomiyosit eldesi yapılabilmektedir. 
  5. Gerçek Zamanlı PZR analizleri: SYBR® Green ile Gerçek Zamanlı PZR analizleri gerçekleştirilmektedir. cDNAlerin ve primer karışımlarının kullanıcı tarafından teslim edilmesi gerekmektedir. 15 ul’lik reaksiyon başına ücretlendirilir. İstenmesi durumunda ayrıca hücre ve doku örneklerinden mRNA izolasyonu, kalite karakterizasyonu, ve cDNA sentezi yapılabilir.