INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison
Abstract
:1. Introduction
2. Results
2.1. Literature Review of INTACT and FANS/FACS Studies
2.2. Assessing Differences in Speed and Sorting Efficiency between FANS and INTACT
2.3. Quantification of Morphological Attributes: FANS- and INTACT-Nuclei in Comparison to INPUT-Nuclei
2.4. Structural and Optical Modifications Observed under Phase-Contrast Microscopy and Fluorescence Microscopy
2.5. Transcriptional Differences of Low-Input RNA-Seq from FANS-Nuclei vs. INTACT-Nuclei
2.6. ATAC-Seq Reveals Differences in Chromatin Accessibility State between FANS- and INTACT-Nuclei
3. Discussion
3.1. Physiological Differences between INTACT- and FANS-Nuclei
3.2. Molecular Differences between FANS-and INTACT-Nuclei
4. Materials and Methods
4.1. Literature Review of INTACT FANS/FACS Studies
4.2. Animals and Ethics Statement
4.3. Tamoxifen Injection and Behavioral Experiments
4.4. Nuclei Isolation from Different Brain Regions
4.5. sfGFP Positive Nuclei Separation
4.5.1. INTACT
4.5.2. FANS
4.5.3. Purity Analysis of INTACT- and FANS-Nuclei
4.6. Parallel Processing of INTACT- and FANS-Nuclei
4.7. Microscopy
4.8. RNA Isolation and nucRNA-Seq Library Preparation
4.9. RNA-Seq Data Analysis
4.10. ATAC-Seq Library Preparation
4.11. ATAC-Seq Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Brain Region\Property Tested | Nuclei Yield (×104/mL) | Total Volume (μL) | Input Nuclei sfGFP+% | Actual 5k Nuclei/Sample (mins) | Theoretical 50k Nuclei/10 Samples (mins) | sfGFP+ Nuclei Yield from INTACT | ||||
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FANS | INTACT | FANS | INTACT | GFP% Supernatant | Yield % | Purity | ||||
Small–medium brain regions | ||||||||||
Nucleus accumbens | 73 | 300 | 18.95 | 2 | 35 | 200 | 60 | 16.5 | 15 | 98.5 |
Hypothalamus | 60 | 400 | 12.8 | 3 | 35 | 300 | 60 | 7.6 | 44 | 98.2 |
Pituitary | 140 | 400 | 47.45 | 1 | 35 | 100 | 60 | 28.9 | 40 | 99.1 |
Hippocampus | 136 | 400 | 23 | 1.5 | 35 | 150 | 60 | 12.3 | 50 | 99.8 |
Large brain regions | ||||||||||
Neocortex 1 | >200 | 900 | 29.3 | - | - | - | - | 3.6 | 87 | 98.5 |
Neocortex 2 | >200 | 900 | 26.7 | - | - | - | - | 3.7 | 86 | 93.6 |
Parameter Compared | INTACT | FANS |
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Experimental approach |
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Processing speed |
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Quantification accuracy |
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Tissue/cellular amounts requirement |
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Effect on nuclear structure |
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Transcriptional alterations |
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Chromatin accessibility alteration |
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Cost |
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Chongtham, M.C.; Butto, T.; Mungikar, K.; Gerber, S.; Winter, J. INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison. Int. J. Mol. Sci. 2021, 22, 5335. https://doi.org/10.3390/ijms22105335
Chongtham MC, Butto T, Mungikar K, Gerber S, Winter J. INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison. International Journal of Molecular Sciences. 2021; 22(10):5335. https://doi.org/10.3390/ijms22105335
Chicago/Turabian StyleChongtham, Monika Chanu, Tamer Butto, Kanak Mungikar, Susanne Gerber, and Jennifer Winter. 2021. "INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison" International Journal of Molecular Sciences 22, no. 10: 5335. https://doi.org/10.3390/ijms22105335