Nature is the power

Single cell RNA sequencing

Bentolhoda Fereydouni

Postdoctoral studies

Single cell RNA sequencing

Department and organisational affiliation:

About me

I am a scientist with a broad and deep experiences  within genomics (Next generation sequencing ).  Current focus  single cell RNA-seq with 10x chromium.

Interests :

• NGS  (Next generation sequencing)   •Single cell RNA Sequencing   • 10x Chromium

• Single cell RNA seq data analysis    • CITE-seq

Research description

My research is focusing on single cell RNA seq for pain behaviour . Pain is the most common problem in the patients with rheumatoid arthritis (RA) and mostly interpreted as a marker of inflammation, the correlation between pain intensity and measure of peripheral inflammation still not complete understood. It is very necessary to understand the mechanism of pain in inflammatory arthritis. With the help of  single cell RNA (ScRNA) sequencing technology with using novel computational approaches including multiple transcriptomic subpopulations we are going to find out more about pain  in RA patients. 

Teaching portfolio

- 5 weeks pedagogical course in Teaching and learning in Higher Education Grundläggande högskolepedagogik, distans (GHPD). Karolinska Institute. 2019 .

- Supervising master student for the project “Identification  of cancer stem cells in Sarcoma”. Gothenburg University, 2017. 

- Instructor of immunohistochemistry laboratory course for Master students of Developmental, Neural, and Behavioral Biology, Goettingen , Germany . WS 2011/2012- WS 2012-2013& WS 2013-2014 .

- Supervising master student for the project “Immunohistochemical analysis of cultured newborn marmoset ovaries”. Georg-August-University Goettingen, Germany. 2013.

- Volunteering teaching to the international students in Goettingen, Germany. XLAB (is an experimental laboratory for young people and bridges the gap between university and high school). Summer 2012.

Education

Karolinska Institute              Stockholm , Sweden , 2018- now

Postdoc-Scientist

- Working with Single cell RNA sequencing and bioinformatic analysis

Methods:

- Single cell 10x Chromium , Next generation sequencing (NGS), FACS , sorting , Data analysis with SPSS and Graph-pad , Animal surgery , 3D  human skin culture , histology, ElISA, qPCR, RNA isolation and advanced confocal microscopy.

University of  Gothenburg    Gothenburg , Sweden, 2016 -2018.           

Postdoc-Scientist

- Experimental systems: Tumor cell lines, and xenograft models.

- Methods: Epigenetic studies, protein–protein interaction studies using immunoprecitpitation , Chromatin immunoprecipitation (ChIP-seq), Next generation sequencing (NGS), ChIP-qPCR, advanced microscopy, cell culture, histology , qPCR

- Bioinformatic analysis for Chip-seq data  

TATAA biocentre /Cambridge University ( Babraham Institute, Epigenetics) 

Gothenburg , Sweden/ Cambridge, UK , 2015-2016

 Marie-Curie Scientist

Innovative techniques and models to understand epigenetic regulation in the pathogenesis of common diseases. Methods : DNA methylation on single cells(Sarcoma and human oocytes), Next generation Sequencing (NGS) , Bioinformatic analysis for DNA methylation on single cell level.

Georg-August-University Göttingen      

German Primate Center (DPZ), Göttingen, Germany        

 Ph.D. / Dr.rer.nat  Biology in Stem cells Department . 

Thesis: In situ and in vitro analysis of germ and stem cell marker-positive cells in the postnatal ovary of the common marmoset monkey

Advisor: Prof. Dr. Rüdiger Behr

 For the first time I could we show that the neonatal marmoset ovary has an extremely immature histological appearance compared with the human ovary and  contains numerous oogonia expressing the pluripotency factors OCT4A, SALL4, and LIN28A (LIN28). The pluripotency factor-positive germ cells also express the proliferation marker Ki-67, which has previously been shown in the human ovary to be restricted to premeiotic germ cells.

With this study I could  introduce the marmoset monkey as a non-human primate model to experimentally study the aspects of primate primitive gonad development, follicle assembly, and germ cell biology in vivo.

I also for the first time established a culture system being stable for more than 20 passages and 5 months. Importantly, comparative transcriptome analysis of the cultured cells with neonatal ovary, embryonic stem cells, and fibroblasts revealed a lack of germ cell and pluripotency genes indicating the complete loss of oogonia upon initiation of the culture. From passage 4 onwards, however, the cultured cells produced large spherical, free-floating cells resembling oocyte-like cells (OLCs). OLCs strongly expressed several germ cell genes and may derive from the ovarian surface epithelium.

I could introduce novel primate ovarian cell culture which initially lacked detectable germ cells but then produced OLCs over a long period of time. This culture system may allow a deeper analysis of early phases of female primate germ cell development and—after significant refinement—possibly also the production of monkey oocytes.            

Academic honours, awards and prizes

- Stiftelsen Konung Gustaf V:s 80-årsfond ( The King Gustaf 80th foundation -Sweden King-house ) 110,000 SEK stipendium  for the project :  ScRNA-seq of Macrophages in DRGs for Therapeutic Treatments in Patients with Rheumatoid Arthritis. 2020

- Karolinska Institute travel grant period 2 and 3  for for visiting collaboration partner University College London, UK for developing method Single cell RNA seq from human CSF. 2019

- Assar Gabrielssons Foundation, 105,500 SEK  for the project “The FET oncogenes in sarcomas and Interactions with SWI/SNF protein complex”. 2017(Online link) & 2016(Online link) .

- Johan Janssons Foundation, 121,000 SEK for the project “The FET oncogenes in sarcomas and Interactions with SWI/SNF protein complex”. 2017(Online link).&2016

- MARIE CURIE Fellowship as part of the EU-funded project Epigenetic Training Network - Innovative techniques and models to understand epigenetic regulation in the pathogenesis of common diseases (EPITRAIN). 2015 .

- DAAD (German Academic Exchange Service) scholarship for PhD study in Germany.

- Singapore International Graduate Award (SINGA), National University of Singapore. 2010  

- Travel grant from Temasek Life Sciences Laboratory, Singapore. February 2009. 

 

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