Protocols
General
- Koehler illumination and DIC configuration for inverted and upright microscopes
- All HCBI coverslip corrected objectives are corrected for #1.5 Coverslips. Please ensure you are ONLY using #1.5 slips.
- The HCBI recomends Prolong Glass (hard mount) or Slow Fade Glass (soft mount) mounting media. We do NOT recomend using moutning media with DAPI pre-mixed into it. This causes substantial background. Nuclear dyes should be applied with/after your secondary antibodies and washed extensively before mounting.
Lightsheet
- Lightsheet consumables(HCBI recommended suppliers)
- Guide to Lightsheet sample prep (Zeiss)
- Click here to view a video of Lightsheet sample prep (Zeiss)
- Guide to stitching tiles with Arivis software
MERSCOPE
- Gene Panel Design - This is completed on the Vizgen website and is at minimum a 4-6 week process. A guide to the Gene panel Design can be found here.
- The HCBI does NOT provide any reagents or equipment required for sample prep. A list of all required general lab reagents and equipment can be found here.
- A list of reagents/equipment to order from Vizgen can be found here (from Dec 2021, prices subject to change).
- The sample prep protocol can be found here.
- A video introduction to the Vizgen Vizualizer software can be found here.
Tissue Clearing
- Clearing with CLARITY and the X-CLARITY ETC system
- Immunostaining for cleared tissue (from Renier et al., Cell, 2016)
Axio Scan
Bruker Lightsheet
Expansion Microscopy
ELYRA
STEDYCON
STED Sample Preparation and Labeling Guide
PALM Laser Microdissection
- Immunohistochemistry on frozen sections prior to microdissection and RNA extraction
- Sample staining, mounting, and cutting for RNA extraction
- Quickguide to PALM microdissection consumables
- RNA extraction from formalin fixed paraffin embedded (FFPE) sections
- RNA extraction from frozen sectionsImmunofluorescence on frozen sections
LSM 780/880
ZEN