Spatial Transcriptomics for OCT using 10x Genomics Visium

Andrew Houston, Siqi Chen, Feng Chen

Published: 2023-01-27 DOI: 10.17504/protocols.io.x54v9d3opg3e/v1
AI 解读
浏览 1207

Abstract

To detect gene expression spatially mapped across a fresh-frozen tissue sample adapted from 10x Genomics Visium protocol.

Steps

Visium Fresh-Frozen

1.

Start here

If performing OCT tissue embedding for the first time be sure to consult pgs.5-9

If utilizing a new tissue type for the first time be sure to utilize the Tissue Optimization Guide which can be found here

2.

RNA extraction and assessment is outlined in the above guide but not always necessary

Most OCT blocks have preserved RNA quality well due to their preservation/storage

3.

Perform all fixation/H&E staining/imaging steps on the Visium Spatial Gene Expression Slide (PN-2000233)

Utilize the guide here

Typically it is not necessary to utilize a coverslip while imaging

4.

Immediately proceed to the Visium Library Construction

Start on pg. 35 using this guide here

5.

Sequence the libraries according to the requirements on pg. 59 of CG000239

推荐阅读

Nature Protocols
Protocols IO
Current Protocols

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Inducible mouse models of colon cancer for the analysis of sporadic and inflammation-driven tumor progression and lymph node metastasis

An unbiased method for evaluating the genome-wide specificity of base editors in rice

Antigen retrieval and clearing for whole-organ immunofluorescence by FLASH

Designing and executing prime editing experiments in mammalian cells

Design and application of the transformer base editor in mammalian cells and mice

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Routine culture and study of adult human brain cells from neurosurgical specimens

Simultaneously measuring the methylation of parent and daughter strands of replicated DNA at the single-molecule level by Hammer-seq

Spatial visualization of comprehensive brain neurotransmitter systems and neuroactive substances by selective in situ chemical derivatization mass spectrometry imaging

查看全部

扫码咨询