RNA Detection

3.4 smFISH 1. Take coverslips with sections from
^80 C and place them in a 6-well plate (Fig.3e). Post-fix the sections in 4% f ...

Image your samples on an epifluorescence microscope with a high NA objective and a sensitive camera (seeNotes 6and 33 ) (Fig.1b ...

your original membrane images. Open the image that ends on “_scaled” in Fiji and duplicate the first channel using the “Duplicat ...

by breaking excessive lines by pressing the left mouse button and the Alt key simultaneously. Go to “Label inspection” mode to c ...

Fig. 6The Transcript analysis plugin. (a) User interface for the Transcript analysis plugin. Before running the Transcript analy ...

Rerun the Cell transcript analysis pipeline with the identified transcript detection threshold (seeNote 43). Check the file tha ...

4 Notes We use Eppendorf caps to embed our samples. Alternatively, commercial molds can be used but we prefer the small size of ...

have also obtained good results with a 601.3NA silicon objective. It is also possible to image your samples on a spinning disk ...

blade temperatures of around
20 C for many other sample types on the same cryostat. After mounting the cryo-block to the spec ...

conditions to your aliquot of proteinase K since excessive pro- tein digestion will affect sample integrity. If signal/noise is ...

samples. Details on how to do this can be found on the follow- ing webpage: “tinyurl.com/KNIME-MS-ECS”. The downsampling factor ...

(‘.log’), and a scatter plot that indicates which spots have been identified as transcripts and which have been identified as fo ...

Chapter 10 Super-Resolution Single Molecule FISH at theDrosophila Neuromuscular Junction Joshua S. Titlow, Lu Yang, Richard M. P ...

tiled oligonucleotides sets are designed to bind to nonoverlapping regions of a transcript. The large number of probes means tha ...

user-friendly commercial solution, namely the spot counting algo- rithm in Imaris. We found that all three programmes performed ...

(Optional) for immunohistochemistry: appropriate primary and secondary antibodies diluted in Wash buffer. (Optional) to counter ...

Extend the incision along the dorsal midline toward the posterior end, then from the centre towards the anterior end of the lar ...

3.5 Mounting 1. Remove the wash buffer and incubate tissue in Vectashield for several minutes (seeNote 5). Place thin strips of ...

5.htmland at the installation instructions. This client-server software integrates visualization, data mining, and image anal- y ...

Create and highlight figures from typical data sets using OMERO.figure (video http://figure.openmicroscopy.org/ videos.html). O ...