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stlearn spatial transcriptomics analysis software  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc stlearn spatial transcriptomics analysis software
Developing and assessing protocols to perform spatial <t>transcriptomics</t> to capture thousands of genes in FFPE cancer tissue. (A) Poly(A)‐capture required the optimisation of tissue permeabilisation step. Probe‐capture required a tissue adherence test. (B) Optimisation for tissue multiplexing and sectioning thickness. (C) Tissue stainning was processed in different conditions in two protocols. (D) Decrosslinking was performed in the same way. (E) In permeabilisation, the mRNA molecules or hybridised probes were released from cells and bound to the spatial oligos on the glass slide. Reverse transcription produced cDNA products in poly(A)‐capture protocol or extended probes in probe‐capture protocol. (F) Eluting captured molecules/probes and preparing the library for long/short cDNA sequencing.
Stlearn Spatial Transcriptomics Analysis Software, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Developing and assessing protocols to perform spatial transcriptomics to capture thousands of genes in FFPE cancer tissue. (A) Poly(A)‐capture required the optimisation of tissue permeabilisation step. Probe‐capture required a tissue adherence test. (B) Optimisation for tissue multiplexing and sectioning thickness. (C) Tissue stainning was processed in different conditions in two protocols. (D) Decrosslinking was performed in the same way. (E) In permeabilisation, the mRNA molecules or hybridised probes were released from cells and bound to the spatial oligos on the glass slide. Reverse transcription produced cDNA products in poly(A)‐capture protocol or extended probes in probe‐capture protocol. (F) Eluting captured molecules/probes and preparing the library for long/short cDNA sequencing.

Journal: The Journal of Pathology

Article Title: Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues

doi: 10.1002/path.6383

Figure Lengend Snippet: Developing and assessing protocols to perform spatial transcriptomics to capture thousands of genes in FFPE cancer tissue. (A) Poly(A)‐capture required the optimisation of tissue permeabilisation step. Probe‐capture required a tissue adherence test. (B) Optimisation for tissue multiplexing and sectioning thickness. (C) Tissue stainning was processed in different conditions in two protocols. (D) Decrosslinking was performed in the same way. (E) In permeabilisation, the mRNA molecules or hybridised probes were released from cells and bound to the spatial oligos on the glass slide. Reverse transcription produced cDNA products in poly(A)‐capture protocol or extended probes in probe‐capture protocol. (F) Eluting captured molecules/probes and preparing the library for long/short cDNA sequencing.

Article Snippet: Datasets supporting this manuscript are available at Zenodo, DOI: https://doi.org/10.5281/zenodo.8053920 and code supporting this manuscript used our stLearn spatial transcriptomics analysis software available at https://stlearn.readthedocs.io/en/latest/ .

Techniques: Multiplexing, Staining, Reverse Transcription, Produced, Sequencing