Nov 29, 2021

Public workspaceTargeted Expansion Sequencing Protocols V.3

DOI
dx.doi.org/10.17504/protocols.io.b2e4qbgw
  • 1McGovern Institute, MIT;
  • 2Harvard-MIT Program in Health Sciences and Technology;
  • 3Human Tumor Atlas Pilot Project;
  • 4Massachusetts Institute of Technology;
  • 5Faculty of Engineering, Gonda Brain Research Center and Institute of Nanotechnology, Bar-Ilan University;
  • 6Broad Institute of MIT and Harvard;
  • 7Department of Biological Engineering, MIT;
  • 8Department of Media Arts and Sciences, MIT;
  • 9Koch Institute for Integrative Cancer Research, MIT;
  • 10Howard Hughes Medical Institute;
  • 11Department of Brain and Cognitive Sciences
  • Ed Boyden: Corresponding author;
  • NCIHTAN
Anubhav Sinha
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DOI: dx.doi.org/10.17504/protocols.io.b2e4qbgw
External link: https://pubmed.ncbi.nlm.nih.gov/33509999/
Collection Citation: Anubhav Sinha, Yi Cui, Shahar Alon, Fei Chen, Asmamaw T. Wassie, Ed Boyden 2021. Targeted Expansion Sequencing Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.b2e4qbgwVersion created by Anubhav Sinha
License: This is an open access collection distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this collection and it’s working
Created: November 29, 2021
Last Modified: November 29, 2021
Collection Integer ID: 55484
Keywords: in situ sequencing, expansion sequencing, targeted ExSeq, ExSeq, spatial transcriptomics, spatially resolved transcriptomics, spatial omics,
Disclaimer
This protocol collection is shared under the HTAN Internal Data and Materials Sharing Agreement and is provided as is. See section 14 of full agreement for full details.

This protocol is shared as an Open Access protocol (under HTAN's definitions). This protocol is Subject to IP Restrictions.
Abstract
This protocol collection accompanies accompanies Expansion Sequencing (ExSeq), covering the four key steps of a targeted Expansion Sequencing (targeted ExSeq) experiment: (1) Padlock probe design; (2) tissue preparation and expansion; (3) library preparation; and (4) in situ sequencing with the Illumina chemistry.

For further details, consult the relevant protocols within the collection. These protocols were used to profile human metastatic breast cancer biopsies as a part of the Human Tumor Atlas Pilot Project (HTAPP).
Image Attribution
All images (c) Massachusetts Institute of Technology.
Materials
See individual protocols for materials.
This protocol collection is shared under the HTAN Internal Data and Materials Sharing Agreement and is provided as is. See section 14 of full agreement for full details.

This protocol is shared as an Open Access protocol (under HTAN's definitions). This protocol is Subject to IP Restrictions.
Files
Protocol
Icon representing the file Targeted ExSeq -- Probe Generation
Name
Targeted ExSeq -- Probe Generation
Version 2
, MIT
Anubhav SinhaMIT
Protocol
Icon representing the file Targeted ExSeq -- Tissue Preparation
Name
Targeted ExSeq -- Tissue Preparation
Version 2
, MIT
Anubhav SinhaMIT
Protocol
Icon representing the file Targeted ExSeq -- Sequencing Library Preparation
Name
Targeted ExSeq -- Sequencing Library Preparation
Version 1
, MIT
Anubhav SinhaMIT
Protocol
Icon representing the file Targeted ExSeq -- In Situ Sequencing (Illumina Chemistry) 
Name
Targeted ExSeq -- In Situ Sequencing (Illumina Chemistry) 
Version 1
, Massachusetts Institute of Technology
Yi CuiMassachusetts Institute of Technology