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HE stain

Definition

Name

Hematoxylin and eosin stain (or haematoxylin and eosin stain or hematoxylin-eosin stain) is often abbreviated as H&E stain or HE stain.

Application

It is one of the principal tissue stains used in histology.

Purpose

  1. Differentiate between the nuclear and cytoplasmic parts of a cell
  2. Overall patterns of coloration from the stain show the general layout and distribution of cells
  3. Provide a general overview of a tissue sample's structure
  4. Biopsy of a suspected cancer

Step

  1. Hematoxylin stains cell nuclei a purplish blue
  2. Eosin stains the extracellular matrix and cytoplasm pink, with other structures taking on different shades, hues, and combinations of these colors

Spatial transcriptomics (Visium)

official website

HE stain

  1. A freshly frozen tissue section attached onto our chip
  2. The tissue section is imaged in order to retrieve histological information.

The Array

The chip contain an array of distinguishable capture probes. The Poly-T tails of these capture probes can bind the Poly-A tails of RNA molecules.

Tissue fixtion

Fix tissue on the chip

Permeabilisation

  1. The tissue is permeabilised with our Permeabilising Reagent which means that small holes in the cell membrane are created
  2. RNA molecules can exit the cells through these and bind to the adjacent capture probes on the chip
  3. The following steps are needed to translate the information stored in the captured RNA molecules as data.

cDNA Synthesis

  1. Create stable double stranded DNA molecules. This is necessary because cDNA-RNA-hybrids are degraded

Library Preparation

  1. The cDNA-RNA-hybrids are cleaved off the chip

Massively Parallel Sequencing

The created libraries are sequenced. Thereby information on what gene the captured RNA was coding for and where in the tissue the RNA came from is extracted.

Imgae-based spatial transcriptomics

Advantage

  1. Map the sub-micrometre-scale intercellular organization of the transcriptome
  2. Characterizing both large numbers of cells and centimetre-scale tissue architectures.
  3. Imaging RNAs within their native context, it is sometimes possible to limit RNA loss Hence, it has high detection efficiencies and low detection limits, important sets of functionally relevant but lowly expressed genes to be characterized.

Application

  1. Providing insights into gene regulatory modules from co-variation in gene expression;
  2. Mapping the internal organization of the transcriptome
  3. Empow- ering all-optical screening methods by linking genetic perturbations to synthetic RNA barcodes52–58;
  4. Inferring aspects of cellular state from RNA-velocity-like measure- ments of nuclear to cytoplasmic RNAs50
  5. Jointly mapping the internal distribution of RNAs and proteins