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Spatial Gene Expression for FFPE

Product Description
Case Analysis
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Sample delivery
Q&A

Considering traditional spatial transcriptome sequencing is limited to fresh frozen tissue sections, 10X Genomics introduces the new Visium spatial gene expression solution for FFPE samples (formalin-fixed paraffin-embedded), which breaks the barriers to obtain spatial gene expression information from FFPE tissue samples and get highly sensitive and specific expression and spatial location information of relevant genes from FFPE samples. FFPE sample gene expression is a pioneering solution that complements traditional pathology-driven analysis, enabling true discovery in a morphological context and further expanding the possibilities of spatial biology research.

 

 

Technical principle

Visium FFPE Spatial Gene Expression is based on the principle of probe hybridisation to obtain a spatial gene expression profile of tissue from FFPE tissue samples, enabling true in situ detection in a morphological context. First, the FFPE tissue sections are placed on a Visium GeneChip for histomorphological staining and imaging, followed by quantitative expression using probes on the Visium GeneChip. The Visium spatial gene expression solution for FFPE samples does not allow for mRNA capture using the poly(dA) sequences of intact mRNAs in fresh frozen tissue samples, due to the high level of RNA degradation that is often associated with FFPE samples. The solution is using paired RNA template-linked probes (RTL) targeting the coding gene to hybridise to the mRNA, with the left probe (LHS) having a partial Read 2 sequence and the right probe (RHS) having a synthetic poly(A) sequence, and the left and right probes hybridising to each other after the mRNA is degraded by RNase. Through tissue permeabilisation, the linked pairs of probes are captured with primer sequences containing Barcode, UMI and poly(dT) sequences on the microarray. The probe sequences carrying the spatial Barcode are then used for library construction and sequencing to obtain gene expression information and spatial location information.

 

探针捕获图

 

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FFPE样本空间转录组测序芯片原理

 

Sample types: human, mouse FFPE samples.

 

Experimental process

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FFPE样本空间转录组测序实验流程

 

Analysis process

FFPE sample space transcriptome sequencing analysis process

 

Application directions

a. Tumor heterogeneity;

b. Histomorphology;

c. Tissue developmental mechanisms;

d. Response to therapeutic intervention;

e. Biomarker discovery;

f. Cellular mapping.

Product advantages

a.Reusing preserved or biobank  samples for biomarker discovery, allowing retrospective and follow-up studies;

b. Using RNA template ligation (RTL) probes ensures high sensitivity and specificity for reliable gene detection results;

c. Combining with immunofluorescence techniques to visualise protein and gene expression, or combine with HE staining for morphological studies;

d. Entire FFPE sections can be studied, eliminating analytical limitations associated with predefined regions of interest and not missing important biological information.

Stay tuned for further updates...

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Space Transcription Histogram of Human Breast Ductal Carcinoma FFPE Sample

Notices of samples delivery

1. Sample type: only human and mouse FFPE samples are supported currently.

2. Transportation condition: 4°C .

Q1: In addition to human and mouse FFPE samples, does spatial transcriptome sequencing support FFPE samples from other species?

A: No. The Visium FFPE spatial gene expression solution is designed to target human and mouse genes with a pair of capture probes covering 18,000 genes in human and 20,000 genes in mouse.

Q2: Does Visium analysis need to be optimised for tissue?

A: The Visium spatial gene expression solution for FFPE does not require tissue optimisation. However, the Visium spatial gene expression solution for fresh frozen samples requires tissue optimisation due to the differences in chemistry and molecular biology between the two sample preparation processes.

Q3: Are the spatial transcriptome sequencing data from FFPE samples reliable compared to fresh frozen tissue samples?

A: Officially, A Visium analysis by 10x Genomics of FFPE in mouse brains and fresh frozen tissues showed a high degree of correlation between the two tissues, demonstrating the reliability and sensitivity of the Visium FFPE spatial gene expression solution.

  • Instructions for single cell sequencing and sample delivery of Wuhan Biological Sample Bank

    Instructions for single cell sequencing and sample delivery of Wuhan Biological Sample Bank
    File size: 360KB 发布时间: 2022-03-10

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