We thank Valeria Fernandez-Vallone for the original instructions for the Miltenyi Neural Dissociation kit. We also thank the Genomics Technology Platform of the Max Delbrueck Centrum for providing the recipe for the NP40 lysis buffer and valuable advice setting up this protocol. We also thank Margareta Herzog and Alexandra Tschernycheff for the lab organizational support.

The described protocol is performed in a biosafety level 1 laboratory of the Max Delbr&#252;ck Center for Molecular Medicine (approval number: 138/08), in accordance with the requirements and in compliance with EU and national rules on ethics in research.
1. Derivation of forebrain organoids from induced pluripotent stem cells (iPSCs)
NOTE: This protocol was tested for several different iPSC lines cultured in a variety of stem cell media from differen...

Single Cell and Nuclei Extraction from Human Brain Organoids

<ol>
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Transcriptomic analysis of single cells and single nuclei has emerged as a pivotal tool for understanding gene regulatory mechanisms within complex tissues. Both methods enable transcriptome studies of brain organoids. To ensure an overall successful experiment, the quality of the starting material is of high relevance. Therefore, it is necessary to cut the organoids regularly to prevent the formation of a necrotic core26. It is also possible to eliminate this issue with an Air-Liquid Interface cu...

Over the last years, organoid technologies have emerged as a promising tool to culture organ-like tissues1,2,3. Especially for organs that cannot be easily accessed, such as the human brain, organoids offer the opportunity to gain insights into&#160;development and disease manifestation4. As such, brain organoids have been widely used as an experimental model to investigate various human brain disorders, including developmental, psychiatric, or even neurodegenerative diseases4,5,6.
With the advent of single-cell transcriptome profiling technologies, primary human tissues and complex in vitro models could be studied with an unprecedented level of granularity, providing mechanistic insights into gene expression changes on the level of cell subpopulations in health and disease and informing about new putative therapeutic targets7,8,9. The organoid field has progressed by utilizing single-cell transcriptome profiling to assess cellular composition, reproducibility and the fidelity of brain organoid technologies10,11,12. Single-cell RNA-sequencing (scRNA-seq) enabled cell classification and the identification of genetic dysregulation in diseased organoids13,14. Importantly, it is the complexity of organoid tissues that necessitates the implementation of techniques that enable the profiling of individual cells. Characterization of organoids using methods such as bulk transcriptome profiling (bulk RNA sequencing) leads to masked cellular heterogeneity and gene expression profiles which are averaged across all types of cells within the complex tissue, ultimately limiting our understanding of ongoing processes during organoid development in health and disease15,16,17. As scRNA-seq methods continue to advance, an increasing number of atlases are being created, exemplified by resources like the Allen Brain Atlas or the Single cell atlas of human brain organoids by Uzquiano et al.18.
Accomplishing successful scRNA-seq from brain organoids relies on effective isolation and capture of intact cells. As the dissociation of brain organoids to obtain individual cells is based on enzymatic digestion, it can influence gene expression patterns by inducing stress and cell damage19,20. Hence, the dissociation of the tissue into individual cells is the most crucial step. An alternative approach is single-nucleus RNA sequencing (snRNA-seq), which facilitates the enzyme-free extraction of nuclei from both, fresh and frozen, tissue21,22. However, the isolation of nuclei from a tissue poses other challenges such as the enrichment of cell types of interest and the low RNA content of nuclei in comparison to cells.
Transcriptome studies of brain organoids are commonly conducted using scRNA-seq10,18,23. However, the isolation of single nuclei might provide an orthogonal and supplemental method to investigate the transcriptomic profile of organoids. Here, we introduce a toolbox for scRNA- and snRNA-seq for brain organoids and discuss the critical points for obtaining the best quality sequencing data.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1,4-DITHIO-DL-THREIT-LSG., F. D. MOL.-BIOL., ~1 M IN H2O (DTT)</td>
			<td>Sigma</td>
			<td>&#160;43816-10ML</td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 ml DNA low binding tubes&#160;</td>
			<td>VWR</td>
			<td>525-0130</td>
			<td>microcentrifuge tube</td>
		</tr>
		<tr>
			<td>10x Cellranger pipeline&#160;</td>
			<td></td>
			<td></td>
			<td>analysis pipline</td>
		</tr>
		<tr>
			<td>15 ml Falcon</td>
			<td>Falcon</td>
			<td></td>
			<td>Centrifuge tube</td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol (BME)</td>
			<td>Life Technologies</td>
			<td>21985023</td>
			<td></td>
		</tr>
		<tr>
			<td>50 ml Falcon</td>
			<td>Falcon</td>
			<td></td>
			<td>Centrifuge tube</td>
		</tr>
		<tr>
			<td>A83-01</td>
			<td>Bio Technologies</td>
			<td>379762</td>
			<td></td>
		</tr>
		<tr>
			<td>Antibiotic/Antimycotic Solution (100X)</td>
			<td>Life Technologies</td>
			<td>15240062</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Plus Supplement</td>
			<td>Life Technologies</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement without vitamin A</td>
			<td>Life Technologies</td>
			<td>12587010</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin, fatty acid free (BSA)</td>
			<td>Sigma Aldrich</td>
			<td>A8806-5G&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>cAMP</td>
			<td>Biogems</td>
			<td>6099240</td>
			<td></td>
		</tr>
		<tr>
			<td>cAMP</td>
			<td>Biogems</td>
			<td>6099240</td>
			<td></td>
		</tr>
		<tr>
			<td>C-CHIP NEUBAUER IMPROVED</td>
			<td>VWR</td>
			<td>DHC-N01</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell strainer 40 &#181;m</td>
			<td>Neolab</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell strainer 70 &#181;m (white) Nylon</td>
			<td>Sigma</td>
			<td>CLS431751-50EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromium Controller &#38; Next GEM Accessory Kit</td>
			<td>10X Genomics</td>
			<td>1000204</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromium Next GEM Chip G Single Cell Kit, 16 rxns</td>
			<td>10X Genomics</td>
			<td>1000127</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromium Next GEM Single Cell 3&#39; Kit v3.1</td>
			<td>10X Genomics</td>
			<td>1000268</td>
			<td></td>
		</tr>
		<tr>
			<td>Complete,&#160; EDTA-free Protease Inhibitor Cocktaill</td>
			<td>Roche</td>
			<td>11873580001</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>MERCK Chemicals</td>
			<td>0000001722</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12</td>
			<td>Life Technologies</td>
			<td>11320074</td>
			<td></td>
		</tr>
		<tr>
			<td>Dounce tissue grinder set 2 mL complete</td>
			<td>Sigma Aldrich</td>
			<td>10536355</td>
			<td></td>
		</tr>
		<tr>
			<td>Essential E8 Flex Medium</td>
			<td>Life Technologies</td>
			<td>A2858501</td>
			<td></td>
		</tr>
		<tr>
			<td>EVE Cell Counting Slides</td>
			<td>VWR</td>
			<td>EVS-050 ( 734-2676)</td>
			<td></td>
		</tr>
		<tr>
			<td>Foetal bovine serum tetracycline free (FBS)</td>
			<td>PAN Biotech</td>
			<td>P30-3602</td>
			<td></td>
		</tr>
		<tr>
			<td>Geltrex LDEV-Free (coating)</td>
			<td>Life Technologies</td>
			<td>A1413302&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>gentleMACS</td>
			<td>Miltenyi Biotec</td>
			<td></td>
			<td>dissociation maschine</td>
		</tr>
		<tr>
			<td>GlutaMAX supplements</td>
			<td>Life Technologies</td>
			<td>35050038</td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin sodium cell culture tested</td>
			<td>Sigma</td>
			<td>H3149-10KU</td>
			<td></td>
		</tr>
		<tr>
			<td>human recombinant BDNF</td>
			<td>StemCell Technologies</td>
			<td>78005.3</td>
			<td></td>
		</tr>
		<tr>
			<td>human recombinant GDNF</td>
			<td>StemCell Technologies</td>
			<td>78058.3</td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin Solution Human</td>
			<td>Sigma Aldrich</td>
			<td>I2643-25MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Knockout serum replacement</td>
			<td>Life Technologies</td>
			<td>10828028</td>
			<td></td>
		</tr>
		<tr>
			<td>LDN193189 Hydrochloride 98%</td>
			<td>Sigma Aldrich</td>
			<td>130-106-540</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM non-essential amino acid (100x)</td>
			<td>Sigma Aldrich</td>
			<td>M7145-100ml</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2 Magnesium Chloride (1M) RNAse free</td>
			<td>Thermo Scientific</td>
			<td>AM9530G</td>
			<td></td>
		</tr>
		<tr>
			<td>mTeSR Plus</td>
			<td>StemCell Technologies</td>
			<td>100-0276</td>
			<td>stem cell medium</td>
		</tr>
		<tr>
			<td>mTeSR1</td>
			<td>StemCell Technologies</td>
			<td>85850</td>
			<td>stem cell medium</td>
		</tr>
		<tr>
			<td>N2 Supplement&#160;</td>
			<td>StemCell Technologies</td>
			<td>17502048</td>
			<td></td>
		</tr>
		<tr>
			<td>Neural Tissue Dissociation Kit</td>
			<td>Miltenyi Biotec B.V. &#38; Co. KG</td>
			<td>130-092-628</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal Plus</td>
			<td>Life Technologies</td>
			<td>A3582901</td>
			<td></td>
		</tr>
		<tr>
			<td>NextSeq500 system</td>
			<td>Illumina</td>
			<td></td>
			<td>Sequencer</td>
		</tr>
		<tr>
			<td>NP-40 Surfact-Amps Detergent Solution</td>
			<td>Life Technologies</td>
			<td>28324</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS Dulbecco&#8217;s</td>
			<td>Invitrogen</td>
			<td>14190169</td>
			<td></td>
		</tr>
		<tr>
			<td>PenStrep (Penicillin - Streptomycin)</td>
			<td>Life Technologies</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Percoll</td>
			<td>Th. Geyer</td>
			<td>10668276</td>
			<td></td>
		</tr>
		<tr>
			<td>Pluronic (R) F-127</td>
			<td>Sigma Aldrich</td>
			<td>P2443-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>RiboLock RNase Inhibitor</td>
			<td>Life Technologies&#160;</td>
			<td>EO0382</td>
			<td></td>
		</tr>
		<tr>
			<td>Rock Inhibitor (Y-27632 dihydrochloride) SB</td>
			<td>Biomol</td>
			<td>Cay10005583-10</td>
			<td></td>
		</tr>
		<tr>
			<td>SB 431542&#160;</td>
			<td>Biogems</td>
			<td>3014193</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride NaCl (5M), RNase-free-100 mL</td>
			<td>Invitrogen</td>
			<td>AM9760G</td>
			<td></td>
		</tr>
		<tr>
			<td>StemFlex Medium</td>
			<td>Thermo Scientific</td>
			<td>A3349401</td>
			<td>stem cell medium</td>
		</tr>
		<tr>
			<td>StemMACS iPS-Brew XF</td>
			<td>Miltenyi Biotec</td>
			<td>130-104-368</td>
			<td>stem cell medium</td>
		</tr>
		<tr>
			<td>TC-Platte 96 Well, round bottom</td>
			<td>Sarstedt</td>
			<td>83.3925.500</td>
			<td></td>
		</tr>
		<tr>
			<td>TISSUi006-A</td>
			<td>TissUse GmbH</td>
			<td>https://hpscreg.eu/cell-line/TISSUi006-A</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue</td>
			<td>T8154-20ml</td>
			<td>Sigma</td>
			<td></td>
		</tr>
		<tr>
			<td>TrypLE Express Enzyme, no phenol red</td>
			<td>Life Technologies</td>
			<td>12604013</td>
			<td>Trypsin-based reagent</td>
		</tr>
		<tr>
			<td>UltraPure 1M Tris-HCl Buffer, pH 7.5</td>
			<td>Life Technologies</td>
			<td>15567027</td>
			<td></td>
		</tr>
		<tr>
			<td>XAV939</td>
			<td>Enzo Life sciences</td>
			<td>BML-WN100-0005</td>
			<td></td>
		</tr>
	</tbody>
</table>

generation and downstream analysis of single-cell and single-nuclei transcriptomes in brain organoids

Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene expression profiles of individual cells, allowing the capture of cellular diversity. In order to overcome limitations posed by difficult-to-isolate cell types, an alternative approach aiming at recovering single nuclei instead of intact cells can be utilized for sequencing, making transcriptome profiling of individual cells universally applicable. These techniques have become a cornerstone in the study of brain organoids, establishing them as models of the developing human brain. Leveraging the potential of single-cell and single-nucleus transcriptomics in brain organoid research, this protocol presents a step-by-step guide encompassing key procedures such as organoid dissociation, single-cell or nuclei isolation, library preparation&#160;and sequencing. By implementing these alternative approaches, researchers can obtain high-quality datasets, enabling the identification of neuronal and non-neuronal cell types, gene expression profiles, and cell lineage trajectories. This facilitates comprehensive investigations into cellular processes and molecular mechanisms shaping brain development.

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids

We are developing and optimizing organoid models in order to apply them for disease modeling. Our goal is to understand the molecular mechanism underlying the disease development and progression, and we are working in close collaboration with Nikolaus Rajewsky Lab, who is developing and applying the single-cell and spatial technologies in order to understand how the RNA regulate the gene expression in health and disease. In recent years, brain organoids have emerged as experimental and translational platforms for studying patient-specific diseases.Therefore, it's not unsurprising that most recent developments aimed at improving the complexity of brain organoid models. For instance, we are now able to generate brain region-specific organoids and also use brain organoids for multi-organoid assemblies. Also, various methods have been implemented to introduce vascularization and immune cells into brain organoids.Currently, one of the most research-advancing technologies that we're using in this lab is spatial transcriptomics, which allows the assessment of gene expression within intact tissue. This is crucial in understanding how gene expression profiles of different cell types vary in different regions within one tissue. Another recent advancement that has been made is single-cell multiomics, which allows the analysis of multiple modules of a single cell, which gives a more holistic approach in analyzing these cells.We employ brain organoids and single-cell and spatial transcriptomics methods to understand underlying mechanisms of human diseases such as Leigh syndrome and herpes simplex encephalitis. Furthermore, we developed high-resolution and cost-effective spatial transcriptomics methods called Open-ST. We compared and optimized the single-cell and single-nucleus RNA sequencing method to understand how well they perform regarding cell type recovery in brain organoid tissue.

To investigate cell type composition of brain organoids using scRNA-seq and snRNA-seq, brain organoids were harvested after 30 days of culture as organoids at this stage already exhibit neuroepithelial loops consisting of progenitors surrounded by intermediate progenitors and early stage neurons4,18. Monitoring the quality of the organoids throughout growth and culturing is essential for obtaining reliable single-cell and single-nucleus data.
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Watch this Scientific Journal Video about Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids at JoVE.com

Here, we introduce a comprehensive protocol for the generation and downstream analysis of human brain organoids using single-cell and single-nucleus RNA sequencing.

Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene ...

generation-downstream-analysis-single-cell-single-nuclei