Assessing the suitability of iPSC-derived human astrocytes for disease modeling

Patrycja Mulica, Carmen Venegas, Zied Landoulsi, Katja Badanjak, Semra Smajic, Sylvie Delcambre, Jens Schwamborn, Rejko Krüger, Paul Antony, Patrick May, Enrico Glaab, Anne Grünewald, Sandro L. Pereira

Disease modeling with iPSC-derived cultures has proved to be particularly useful, although the selection of an appropriate protocol for a given research question remains challenging. Thus, here, we compared two approaches for the generation of iPSC-derived astrocytes. We phenotyped glia that were obtained using the differentiation protocols by Oksanen or Palm and colleagues, respectively. We employed high-throughput imaging and RNA sequencing to deep-characterize the cultures. Oksanen and Palm astrocytes differ considerably in their properties: while the former cells are more labor-intense in their generation (5 vs 2 months), they are also more mature. This notion was strengthened by data resulting from cell type deconvolution analysis that was applied to bulk transcriptomes from the cultures to assess their similarity with human postmortem astrocytes. Overall, our analyses highlight the need to consider the advantages and disadvantages of a given differentiation protocol, when designing functional or drug discovery studies involving iPSC-derived astrocytes.

Raw data


  • RNA sequencing data was generated at the Beijing Genomics Institute (BGI) in Copenhagen, Denmark, using the BGISEQ-500 platform
  • The dataset contains 2 healthy control cell lines
  • 3 biological replicates of each healthy control-derived astrocytes were sequenced, two methods of astrocyte differentiation were used as described in the manuscript

Technical metadata

  • File formats: FASTQ
  • Total size: 92 GB
  • 24 files, 12 samples

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Derived data

All supplementary data and data behind figures are available here.

Source code

The scripts used to analyse the data are available here.