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Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol

M. Carla Carisì, Owain Howell Orcid Logo, Alwena Morgan Orcid Logo, Jeffrey Davies Orcid Logo

STAR Protocols, Volume: 3, Issue: 4, Start page: 101896

Swansea University Authors: Owain Howell Orcid Logo, Alwena Morgan Orcid Logo, Jeffrey Davies Orcid Logo

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DOI (Published version): 10.1016/j.xpro.2022.101896

Abstract

We describe a modified BaseScope™ Assay protocol (ACDBio) for RNA in situ hybridization on fixed-frozen human brain tissue. The original protocol caused tissue detachment due to harsh tissue pre-treatment. We therefore optimized it to improve tissue stability while providing high stain quality in fr...

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Published in: STAR Protocols
ISSN: 2666-1667
Published: Elsevier BV 2022
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URI: https://cronfa.swan.ac.uk/Record/cronfa65354
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first_indexed 2024-01-04T12:22:55Z
last_indexed 2024-01-04T12:22:55Z
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spelling v2 65354 2023-12-20 Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol 58c995486fc93a242b987640b692db8c 0000-0003-2157-9157 Owain Howell Owain Howell true false 9ea39c3d0935c897cb9fcd3ba550af71 0000-0002-3441-5357 Alwena Morgan Alwena Morgan true false 2cb3d1d96a7870a84d2f758e865172e6 0000-0002-4234-0033 Jeffrey Davies Jeffrey Davies true false 2023-12-20 BMS We describe a modified BaseScope™ Assay protocol (ACDBio) for RNA in situ hybridization on fixed-frozen human brain tissue. The original protocol caused tissue detachment due to harsh tissue pre-treatment. We therefore optimized it to improve tissue stability while providing high stain quality in fragile post-mortem tissue from aged donors with advanced neurodegeneration. The main changes include two additional fixation steps and modifications to the pre-treatment protocol. We also describe tissue imaging and stain quantification using the open-source QuPath software. Journal Article STAR Protocols 3 4 101896 Elsevier BV 2666-1667 2 12 2022 2022-12-02 10.1016/j.xpro.2022.101896 http://dx.doi.org/10.1016/j.xpro.2022.101896 Protocol COLLEGE NANME Biomedical Sciences COLLEGE CODE BMS Swansea University Other 2024-03-22T16:45:38.6850116 2023-12-20T11:04:20.0623304 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Biomedical Science M. Carla Carisì 1 Owain Howell 0000-0003-2157-9157 2 Alwena Morgan 0000-0002-3441-5357 3 Jeffrey Davies 0000-0002-4234-0033 4 65354__29375__51da542e9e4b4602b8384fef9131b459.pdf 65354.pdf 2024-01-04T12:22:04.5601315 Output 4857641 application/pdf Version of Record true Released under a Creative Commons CC-BY-NC-ND license. true eng https://creativecommons.org/licenses/by-nc-nd/4.0/
title Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
spellingShingle Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
Owain Howell
Alwena Morgan
Jeffrey Davies
title_short Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
title_full Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
title_fullStr Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
title_full_unstemmed Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
title_sort Analysis of target mRNAs in the fixed-frozen human brain using a modified BaseScope-ISH Assay protocol
author_id_str_mv 58c995486fc93a242b987640b692db8c
9ea39c3d0935c897cb9fcd3ba550af71
2cb3d1d96a7870a84d2f758e865172e6
author_id_fullname_str_mv 58c995486fc93a242b987640b692db8c_***_Owain Howell
9ea39c3d0935c897cb9fcd3ba550af71_***_Alwena Morgan
2cb3d1d96a7870a84d2f758e865172e6_***_Jeffrey Davies
author Owain Howell
Alwena Morgan
Jeffrey Davies
author2 M. Carla Carisì
Owain Howell
Alwena Morgan
Jeffrey Davies
format Journal article
container_title STAR Protocols
container_volume 3
container_issue 4
container_start_page 101896
publishDate 2022
institution Swansea University
issn 2666-1667
doi_str_mv 10.1016/j.xpro.2022.101896
publisher Elsevier BV
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Biomedical Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Biomedical Science
url http://dx.doi.org/10.1016/j.xpro.2022.101896
document_store_str 1
active_str 0
description We describe a modified BaseScope™ Assay protocol (ACDBio) for RNA in situ hybridization on fixed-frozen human brain tissue. The original protocol caused tissue detachment due to harsh tissue pre-treatment. We therefore optimized it to improve tissue stability while providing high stain quality in fragile post-mortem tissue from aged donors with advanced neurodegeneration. The main changes include two additional fixation steps and modifications to the pre-treatment protocol. We also describe tissue imaging and stain quantification using the open-source QuPath software.
published_date 2022-12-02T16:45:37Z
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score 11.01353

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