Dryad DOI: https://doi.org/10.5061/dryad.6m905qgcm

Oligodendrocytes, the myelinating cells of the central nervous system (CNS), are essential for the formation of myelin sheaths and pivotal for maintaining axonal integrity and conduction. Disruption of these cells and the myelin sheaths they produce is a hallmark of demyelinating conditions like Multiple Sclerosis or resulting from certain drug side effects, leading to profound neurological impairments. In this study, we created a human brain organoid comprising neurons, astrocytes, and myelinating oligodendrocytes. By integrating iPSC-derived microglia, we endowed the brain assembloid with immune characteristics. Our model enabled the investigation of demyelination and remyelination - a process in which myelin sheaths are regenerated - in a human context. Our findings reveal that the integrated microglia were active participants in myelin repair, responding to demyelination with a robust inflammatory response, paving the way for regeneration. This was evidenced by the reduction of myelin following toxin-induced demyelination and subsequent self-driven remyelination.

This data set is a DIA proteomics dataset of two timepoints from human brain organoid samples comprising neurons, astrocytes, and myelinating oligodendrocytes.
The dataset includes the cytosolic and nuclear fractions and biological replicates for each timepoint (N = 3 for week 4 and N = 4 for week 10).

Description of the data and file structure

Spectronaut output

The file "neuronal_organoids_spectronaut_protein_output.tsv" contains the protein-level spectronaut output. The most important columns are

• "R.FileName": The sample identifier
• "PG.ProteinGroups" The protein group identifier
• "PG.Quantity": The protein abundance values
• Additional columns provide information on quantification details and protein annotation as described in the Spectronaut documentation

Filtered data used for analysis

The files prefixed neuronal_organoids_data_filtered contain the data matrices, features, and sample annotations that were used for analysis. They have the following content

• "neuronal_organoids_data_filtered_sample_annotation.tsv": the sample (column) annotation of the expression matrix. Row names of this file correspond to column names in the above data matrix. Columns in this file contain sample characteristics such as the sampling time.
  • SampleName: the sample identifier used in the protein abundance .gct files described below
  • group: the sample grouping (fraction and timepoint)
  • fraction: indicates whether the sample is from the nuclear or cytosolic fraction
  • week: a numeric for the collection time point in weeks
  • collection_time_point: the collection week as a character
  • Replicate: the replicate within the sample groups
  • specimen_description: HMBO
  • specimen_type: Organoids
  • readout_id: the raw file name for each sample
  • SampleDynamicRange: dynamic range across all proteins per sample
  • SampleMedian median: across all protein abundances per sample
  • PctProteinQuantifiable: Percentage of proteins quantified per sample
• "neuronal_organoids_data_filtered_feature_annotation.tsv": the protein group (row) annotation of the expression matrix. Row names of this file correspond to row names in the above data matrix. Columns in this file contain protein information such as the number of unique peptides, peptide sequence, and protein annotation.
  • FeatureID: the row identifier used in the protein abundance .gct files described below. It also corresponds to "PG.ProteinGroups" in the Spectronaut output file. Protein groups can consist of more than one UniProt identifier, separated by ";".
  • Accession: first UniProt identifier of FeatureID
  • AdditionalAccessions: if exist, all other UniProt identifiers of FeatureID, otherwise NA
  • Description: gene description of the protein group
  • GeneName: corresponding gene name(s) of proteins in a protein group
  • ProteinName: the protein name(s) of proteins in a protein group
  • Organism: which organism a protein group was mapped to
  • UniquePeptides: number of unique peptides per protein group
  • Completeness: average quantification completeness of a protein group across all samples
  • Coverage: percent sequence coverage of a protein group
  • FeatureCV: coefficient of variation of a protein group
  • FeatureDynamicRange: dynamic range of a protein group
  • FeatureMedianAbundance: median abundance of a protein group across samples
• "neuronal_organoids_data_filtered_imputed.gct": the protein abundance matrix in gct format. Rows correspond to protein groups, columns correspond to samples. Row identifiers are the FeatureIDs, column identifiers are the SampleNames. Missing values have been imputed using a mixed strategy (If only one sample is missing for a protein, the median value, 0.5 of the minimum, is imputed).
• "neuronal_organoids_data_filtered_ibaq.gct": ibaq normalized version of the protein abundance matrix above in gct format. Row identifiers are the FeatureIDs, column identifiers are the SampleNames. For protein groups with more than one UniProt identifier, all values possible ibaq values (separated by ";") are given.