Comparison of chemical lysis buffers for condensate extraction
| Publications | Target condensate | Lysed compartment | Lysis buffer | Salts | Detergenta | Organism/cell type |
|---|---|---|---|---|---|---|
| Bornens et al. (1987), Bornens and Moudjou (1998), Andersen et al. (2003), Gogendeau et al. (2015) | Centrosome | Cytoplasm | 1 mM Tris-HCl, pH 8.0 | 0.5 mM MgCl2 | 0.5% IGEPAL CA-630 | KE37 cells |
| Schulz et al. (2006) | Centrosome | Cytoplasm | 100 mM Na-PIPES, pH 6.9 | 2 mM MgCl2 | 0.3% Triton X-100 | Dictyostelium discoideum |
| Carden et al. (2023) | Centrosome | Cytoplasm | 50 mM Tris-HCl, pH 8.0 | 150 mM NaCl | 1% (vol/vol) NP-40, 0.5% (wt/vol) Na-deoxycholate, and 0.1% (wt/vol) SDS | HEK293T |
| Neil et al. (2021) | L-body | Cytoplasm | 10 mM HEPES, pH 7.4 | 100 mM KOAc and 3 mM MgCOAc | 0.05% NP-40 | X. leavis oocyte |
| Hubstenberger et al. (2017), Safieddine et al. (2024) | P body | Cytoplasm | 50 mM Tris, pH 7.4 | 150 mM NaCl | 0.2% Triton X-100 | HEK293 |
| Zhou et al. (2024) b | DHX9 stress granules | Cytoplasm | 50 mM HEPES, pH 7.5 | 150 mM KCl | 1% NP-40 | HeLa |
| Matheny et al. (2019) | Stress granule and P body | Cytoplasm | 50 mM Tris HCl, pH 7.4 | 100 mM KOAc and 2 mM MgOAc | 0.5% NP-40 | U2OS cells |
| Mintz (1999), Saitoh et al. (2004) | Nuclear speckle | Nucleus | 10 mM Tris-HCl, pH 7.4 | 500 mM NaCl and 5 mM MgCl2 | 1% Triton | Swiss Webster female mice liver |
| Reddy et al. (2023) | Paraspeckle | Nucleusc | 10 mM Tris-HCl, pH 7.5 | 150 mM NaCl | 1% Triton X-100 and 0.1% deoxycholate | HEK293FRT |
| An et al. (2019) | Paraspeckle-like | Nucleus | 50 mM Tris HCl, pH 7.4 | 400 mM NaCl, 100 mM KOAc, and 2 mM MgOAc | 0.5% NP-40 | HEK cells |
| Jain et al. (2016), Wheeler et al. (2017) | Stress granules | Cytoplasm | 50 mM Tris HCl, pH 7.4 | 100 mM KOAc and 2 mM MgCOAc | 0.5% NP-40 | Yeast strain BY4741 |
| Publications | Target condensate | Lysed compartment | Lysis buffer | Salts | Detergent | Organism/cell type |
|---|---|---|---|---|---|---|
| Centrosome | Cytoplasm | 1 mM Tris-HCl, pH 8.0 | 0.5 mM MgCl2 | 0.5% IGEPAL CA-630 | KE37 cells | |
| Centrosome | Cytoplasm | 100 mM Na-PIPES, pH 6.9 | 2 mM MgCl2 | 0.3% Triton X-100 | ||
| Centrosome | Cytoplasm | 50 mM Tris-HCl, pH 8.0 | 150 mM NaCl | 1% (vol/vol) NP-40, 0.5% (wt/vol) Na-deoxycholate, and 0.1% (wt/vol) SDS | HEK293T | |
| L-body | Cytoplasm | 10 mM HEPES, pH 7.4 | 100 mM KOAc and 3 mM MgCOAc | 0.05% NP-40 | ||
| P body | Cytoplasm | 50 mM Tris, pH 7.4 | 150 mM NaCl | 0.2% Triton X-100 | HEK293 | |
| DHX9 stress granules | Cytoplasm | 50 mM HEPES, pH 7.5 | 150 mM KCl | 1% NP-40 | HeLa | |
| Stress granule and P body | Cytoplasm | 50 mM Tris HCl, pH 7.4 | 100 mM KOAc and 2 mM MgOAc | 0.5% NP-40 | U2OS cells | |
| Nuclear speckle | Nucleus | 10 mM Tris-HCl, pH 7.4 | 500 mM NaCl and 5 mM MgCl2 | 1% Triton | Swiss Webster female mice liver | |
| Paraspeckle | Nucleus | 10 mM Tris-HCl, pH 7.5 | 150 mM NaCl | 1% Triton X-100 and 0.1% deoxycholate | HEK293FRT | |
| Paraspeckle-like | Nucleus | 50 mM Tris HCl, pH 7.4 | 400 mM NaCl, 100 mM KOAc, and 2 mM MgOAc | 0.5% NP-40 | HEK cells | |
| Stress granules | Cytoplasm | 50 mM Tris HCl, pH 7.4 | 100 mM KOAc and 2 mM MgCOAc | 0.5% NP-40 | Yeast strain BY4741 |
Tendencies here are that cytoplasmic condensates are extracted under mild conditions with light hypotonicity or isotonicity of the buffer and with mild, low-concentrated detergent. One noticeable exception is the centrosome, for which harsher lysis conditions have been used.
HeLa cells were fixed with paraformaldehyde prior to the lysis process.
Nuclear condensates require a high concentration of salt or a more potent detergent. This has to be taken into consideration while examining the results from these papers, as condensates might have been degraded.
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