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Sanderson Center for Optical Experimentation (SCOPE)
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GeoMx Samples
FFPE Protein
Fresh Frozen Protein
FFPE RNA
Fixed Frozen RNA
Fresh Frozen RNA
GeoMx Samples
FFPE Protein
Fresh Frozen Protein
FFPE RNA
Fixed Frozen RNA
Fresh Frozen RNA
GeoMx Samples
GeoMx Sample preparation log
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Sample information
Name
*
Date
User name
Select sample type
*
-- Select an option --
Fresh Frozen RNA
Fixed Frozen RNA
FFPE RNA
Fresh Frozen Protein
Fixed Frozen Protein
FFPE Protein
Sample type selection
Fixed Frozen RNA step
Fresh Frozen RNA
FFPE RNA step
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GeoMx RNA fresh frozen form
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Date
User Name
PI
Sample type
*
Fresh frozen
Fixed Frozen
FFPE
Tissue type
Sample label 1
Sample 2 label
Sample 3 label
Sample 4 label
Morphology markers and concentrations per sample
Reagent preparation
*
95% EtOH (make fresh weekly)
1x PBS in DEPC H2O
Proteinase K solution (10 ul in 200 ml PBS for 1 ug/mL)
NBF stop buffer
2x SSC
4x SSC
1x Tris-EDTA pH9.0 (antigen retrieval solution)
50% EtOH in DEPC H2O
70% EtOH in DEPC H2O
Confirm tissue fits inside usable area
*
Yes - no trimming needed
Trimmed samples to fit
Fixation
10% NBF overnight (12-16 hours) at room temperature
Supplies preparation
Wash all Coplin jars
Wash hyb oven insert
Preheat hyb oven to 60 degrees C
Fresh frozen sample preparation
*
Wash 1 in PBS 2 minutes
Wash 2 in PBS 2 minutes
Wash 3 in PBS 2 minutes
Bake in oven at 60 degrees C for 30 minutes
50% EtOH for 5 mins
70% EtOH for 5 mins
100% EtOH 1 for 5 mins
100% EtOH 2 for 5 mins
Air dry slides 5 mins (up to 1 hour)
Put water and Tris EDTA Coplin jars in steamer
Preheat steamer
Heat ProtK solution in 37 degree water bath
Target retrieval
*
Brain/Breast 20 mins
Cell pellets 15 mins at 85 degrees C
Colorectal 20 mins
Melanoma 20 mins
Mouse tissue 20 mins
NSCLC 20 mins
Prostate tumor
Tonsil 15 mins
Expose RNA targets
1x PBS wash 5 mins (up to 1 hour)
0.1 ug/mL ProtK for 15 mins
1 ug/mL ProtK for 15 mins
1 ug/mL ProtK for 5 mins
1x PBS wash 5 mins
Set up NBF and NBF stop buffer during wash
Postfix
*
10% NBF wash 5 mins
NBF stop buffer 1 5 mins
NBF Stop buffer 2 5 mins
1x PBS 5 mins
In situ hybridization part 1
Warm buffer R and detection probes
Vortex probes and spin down
Clean hyb chamber
Damp kimwipes in chamber
Make hybridization mix
Hybridization mix information
In situ hybridization part 2
Remove slides from PBS 1 at a time and dry
Add 200 uL hybridization solution to each slide
Apply HybriSlip
Incubate overnight at 37 degrees in hyb oven
Stringent washes to remove off target probes
*
Warm 100% formamide to room temperature before opening
Make stringent wash (equal parts 4xSC and 100% formamide)
Fill two coplin jars with stringent wash and put in water bath at 37 degrees
Fill 3 coplin jars with 2XSSC
Dip slides in 2X SSC to allow coverslips to come off
Stringent wash 1 for 25 mins at 37 degrees
Stringent wash 2 for 25 mins at 37 degrees
2x SSC wash 1 - 2 mins
Add morphology markers
*
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Microscopes
Microscopes
Live Cell Imaging
Confocal Imaging
Super Resolution and TIRF
Multiphoton Imaging
Rates
SCOPE Microscopy Sample Submission Form
Leica PIM
Spatial Biology
Spatial Biology
Vizgen MERFISH
Vizgen MERFISH
MERFISH sample submission form
MLSC data request form
NanoString GeoMx
NanoString GeoMx
GeoMx sample submission form
Slide scanning service
Slide scanning service
Slide scanning submission form
TissueFAXS SL Q
TissueFAXS iQ
Data transfer and viewing
Image analysis
FAQs
RNAScope
Spatial Biology Tutorials
Vizgen CSP
Training
Training
General training for all users
Widefield training
Widefield training
Delta Vision microscope training
High speed video microscopes training
Olympus cellTIRF training
Confocal training
Confocal training
Leica SP8 confocal training
FCS training
TIRF training
TIRF training
GE OMX ring TIRF
Olympus cellTIRF
Nikon A1 TIRF
Super resolution training
Super resolution training
Bliq SLAM training
Leica Lightning training
Multi-Photon training
Multi-Photon training
Bliq Multi-Photon inverted microscope
Bliq Upright Multi-Photon microscope
Image Analysis
Image Analysis
Analysis Project submission form
Forms and Resources
Contact US
FAQ
About
About
History
Staff
Publications
Events
Events
Spatial Biology Explorers
Fredric S. Fay lecture
Additional Resources
About
Admissions
Education
Faculty
Research
Diversity
Giving