Home

GPSeq is a technique that aims at generating growing rings of digestion. Here, we aim at confirming such results, providing a systematic pipeline to identify optimal conditions before sequencing the samples.

Introduction

The GPSeq technique uses a restriction enzyme to cut, with different probability, peripheral and central loci in fixed nuclei. The restricted sites are then ligated to a linker, compatible with both imaging and sequencing.

Imaging is generally used as a validation step, to verify that restriction was properly performed and that growing rings of digestion were generated (confirmed by STED). On the other hand, information on the restricted regions sequence can is obtained through sequencing.

Usually, a GPSeq experiment consists of a series of conditions in which the restriction happens with increasing probability towards the nuclear center. Thus, confirming the presence of and characterizing the growing rings of digestions is a necessary step when setting up the method.

Moreover, analysis of FISH signal radial positions can be used to validate the centrality estimated by GPSeq.

Documentation

Use the sidebar on the right to navigate pygpseq docs!

• Introduction to go back to this page.
• Installation for how to setup and maintain the pipeline on your local computer.
• Corresponding script pages for instructions on how to run them.
  • GPSeq image analysis
    • anim: input
    • anim: run
    • anim: output
  • GPSeq FISH analysis
    • fromfish: input
    • fromfish: run
    • fromfish: output
    • fromfish_merge
  • TIFF tools
    • auto3dseg
    • findoof
    • split
    • Un/Compress (tiffcu)
    • Conversion (from: nd2, czi)
• Contributing on how to contribute to pygpseq.