Evidence map›Paper›PMID 37423994›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Spatial Transcriptomics in Kidney Tissue.

Arti M Raghubar, Joanna Crawford, Kahli Jones, Pui Y Lam, Stacey B Andersen, Nicholas A Matigian, Monica S Y Ng, Helen Healy, Andrew J Kassianos, Andrew J Mallett

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
2.5field-weighted citation impact, top 11% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 1 country.

Arti M RaghubarKidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
Joanna CrawfordInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
Kahli JonesInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
Pui Y LamInstitute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
Stacey B AndersenGenome Innovation Hub, University of Queensland, Brisbane, QLD, Australia.
Nicholas A MatigianQCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
Monica S Y NgKidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
Helen HealyKidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
Andrew J KassianosKidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
Andrew J MallettFaculty of Medicine, University of Queensland, Brisbane, QLD, Australia. Andrew.Mallett@health.qld.gov.au.
The University of Queensland · AURoyal Brisbane and Women's Hospital · AUPrincess Alexandra Hospital · AUQueensland Health · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Unlike bulk and single-cell/single-nuclei RNA sequencing methods, spatial transcriptome sequencing (ST-seq) resolves transcriptome expression within the spatial context of intact tissue. This is achieved by integrating histology with RNA sequencing. These methodologies are completed sequentially on the same tissue section placed on a glass slide with printed oligo-dT spots, termed ST-spots. Transcriptomes within the tissue section are captured by the underlying ST-spots and receive a spatial barcode in the process. The sequenced ST-spot transcriptomes are subsequently aligned with the hematoxylin and eosin (H&E) image, giving morphological context to the gene expression signatures within intact tissue. We have successfully employed ST-seq to characterize mouse and human kidney tissue. Here, we describe in detail the application of Visium Spatial Tissue Optimization (TO) and Visium Spatial Gene Expression (GEx) protocols for ST-seq in fresh frozen kidney tissue.

Indexed as

Gene Expression ProfilingKidneyTranscriptomeAnimalsCryopreservationCryoultramicrotomyEosine Yellowish-(YS)FluorescenceHematoxylinHumansMicePermeabilityStaining and LabelingEosine Yellowish-(YS)HematoxylinKidneySpatial transcriptomicsVisium Spatial Gene ExpressionVisium Spatial Tissue Optimization

Identifiers

PMID37423994
OpenAlexW4383710687

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.