/Lattke_et_al_Astrocyte_Maturation

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Lattke_et_al_Astrocyte_Maturation

This repository contains the code used for the analyses in “Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture” by Lattke et al. [[insert doi]]

Code_and_usage_overview.pdf contains a detailed description of the following folders with analysis scripts and related files in this repository:

  • Figure1_scRNA-Seq_striatum: This pipeline was used for the scRNA-Seq analysis of striatal astrocyte maturation (related to Figure 1).
  • Figure2_RNA-Seq_cortex: This pipeline was used for the bulk-RNA-Seq analysis of cortical astrocyte maturation (related to Figure 2).
  • Figure3_ATAC-Seq_in_vivo: This pipeline was used for the bulk-ATAC-Seq analysis of cortical astrocyte maturation (related to Figure 3).
  • Figure4_ATAC-Seq_BMP_astr_vs_in_vivo: This pipeline was used for the bulk-ATAC-Seq analysis of astrocyte maturation in vitro vs in BMP astrocytes in vitro (related to Figure 4).
  • Figure4_RNA-Seq_BMP_astr_vs_in_vivo: This pipeline was used for the bulk-RNA-Seq analysis of astrocyte maturation in vitro vs in BMP astrocytes in vitro (related to Figure 4).
  • Figure5_metabolite_analysis: This pipeline was used for the metabolomic analysis of astrocytes differentiated in vitro overexpressing specific transcription factors (related to Figure 5).
  • Figure5_RNA-Seq_transcription_factor_expression: This pipeline was used for the bulk-RNA-Seq analysis of astrocytes differentiated in vitro overexpressing specific transcription factors (related to Figure 5).
  • Figure6_ATAC-Seq_transcription_factor_expression: This pipeline was used for the bulk-ATAC-Seq analysis of transcription factor expression in vitro vs astrocytes in vivo (related to Figure 6).
  • Figure6_RNA-Seq_Rorb_Fezf2_co-expression: This pipeline was used for the bulk-RNA-Seq analysis of astrocytes differentiated in vitro overexpressing Rorb and Fezf2 in combination (related to Figure 5).
  • Figure7_ATAC-Seq_maturation_signals: This pipeline was used for the bulk-ATAC-Seq analysis of different culture conditions in vitro vs astrocytes in vivo (related to Figure 7).
  • Figure7_RNA-Seq_maturation_signals: This pipeline was used for the bulk-RNA-Seq analysis of different culture conditions in vitro vs astrocytes in vivo (related to Figure 7).
  • FigureS2A_RNA-Seq_cortex_bulk_vs_Str_pseudobulk: This pipeline was used for the pseudo-bulk-RNA-Seq comparison of striatal and cortical astrocyte maturation (related to Figure S2A).
  • FigureS6C_RNA-Seq_BMP_vs_published_in_vitro_astrocytes: This pipeline was used for the comparison of astrocyte maturation in vitro and in vivo with different published astrocyte in vitro models (related to Figure S6C).
  • FigureS8_re-analysis_published_ChIP_vs_astrocyte_ATAC-Seq: This pipeline was used for the comparison of published ChIP-Seq datasets to ATAC- and RNA-Seq data from the transcription factor expression in vitro experiments (related to Figure S8).