Spatial transcriptomics in Flemingsberg!

Spatial transcriptomics techniques are booming! It is now possible to identify where RNAs are located within a tissue! At the LCI facility, we routinely image samples labelled with RNAscope. If you use RNAscope, you might be interested in this workshop where you will learn how to label thick samples with RNAscope, and this symposium about automated RNAscope.

Additionally, we can now offer the 10x Genomics Visium technology on the South Campus, as a collaboration between 4 core facilities in Flemingsberg: LCI, FENO, SICOF and BEA core facilities!

Here is the workflow:

  1. We discuss your project and advise you for the preparation of your sample.
  2. You cut your sample and optimize the antibody or H/E staining yourself, under the guidance if the LCI staff to best preserve the RNAs.
  3. You image your tissue sections at the LCI facility.
  4. You transfer your section to SICOF who tags the RNAs and amplifies the library, using the 10x Genomics Visium technology.
  5. The library goes to BEA for sequencing.
  • Section size: max 6.5×6.5 mm or max 11×11 mm
  • Human or mouse
  • Paraffin-embedded or fresh-frozen
  • Labelled with H/E or fluorescent antibodies

Come and talk to us about your Spatial Transcriptomics project!

Time to register to the LCI microscopy course!

Dear all

It is time to enroll to the yearly light microscopy course run by the Live Cell imaging core facility (29 Jan – 17 Feb 2024): Microscopy: improve your imaging skills – from sample preparation to image analysis’ (6 credits).

  • Check the course schedule 2024 and the syllabus to see the course content and alumni testimonies.
  • Postdocs or registered PhD students can apply to the course.
  • Please read carefully the eligibility criteria in the syllabus and note that the last registration date is the 15th of November.
  • If you cannot apply to the course, you can anyway follow any of the lectures (in blue on the schedule) as they will be publicly broadcasted live on Zoom and accessible to anyone without registration. The schedule and zoom link are on the course page.

The purpose of this course is to enable PhD students and researchers who have already and recently used a microscope to acquire images of fluorescent samples, to improve their microscopy skills.

The course is NOT aimed at training people to use the LCI facility microscopes. The focus is instead on providing the students with enough theoretical and practical knowledge about their OWN sample and their OWN microscope, to enable them to:

1) prepare their sample and formulate their scientific question in a way that is suitable for data extraction from fluorescence images

2) properly use the hardware available in their lab/facility and 3) fully understand each parameter they need to set in the software in their lab/facility.

The aim is to provide the course students with the tools to acquire on ANY wide field, confocal or light sheet microscope, images of their samples that reliably answer their scientific question.

Please help us spread the word. 😃

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