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Script archive: Lineage recording in human cerebral organoids

This repository includes scripts to preprocess the iTracer data, as well as scripts to reproduce analysis done on the paper "Lineage recording in human cerebral organoids". In the paper, we describe iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR/Cas9 scarring, and is compatible with single-cell and spatial transcriptomics. In the paper we also describe how we used the tool to investigate cell lineages in cerebral organoid development.

The paper has been accepted and will be available soon. Its earlier version is available in bioRxiv: Lineage recording reveals dynamics of cerebral organoid regionalization.

Folder description

Folder Description Related figures
analysis_lightsheet The scripts to visualize and analyze the lightsheet nuclei-tracked data, given the data frame derived from the Mastodon-exported XML files. Fig. 3, ExtData Fig. 6
analysis_microdissection The scripts to analyze the scRNA-seq data of the iTracer-ed microdissected cerebral organoid Fig. 5, ExtData Fig. 9
analysis_neuroepithelium The scripts to analyze the scRNA-seq data of the iTracer-ed D15 cerebral organoids Fig. 4, ExtData Fig. 8
analysis_perturb The scripts to analyze the iTracer-perturb data Fig. 6, ExtData Fig. 10
analysis_visium The notebooks and scripts to analyze the visium data of the iTracer-ed cerebral organoids Fig. 2, ExtData Fig. 5
analysis_whole-organoids The scripts to analyze the scRNA-seq data of the iTracer-ed whole cerebral organoids Fig. 1/4, ExtData Fig. 2/3/4/7
convert_mastodon_xml2df The python script to convert the Mastodon-exported XML files to a table for further analysis
ext External gene lists used in the analysis
extract_barcode_scars The codes to extract barcode and scar information from the post-CellRanger BAM files of the barcode/scar cDNA libraries
r_functions The R functions used in the analysis

Related data

The raw data reported in this work can be found in ArrayExpress:

  • E-MTAB-10974: scRNA-seq data of iTracer whole-cerebral-organoid samples
  • E-MTAB-10973: scRNA-seq data of iTracer early cerebral organoid (d15) samples
  • E-MTAB-10972: 10x visium data of iTracer cerebral organoid slices
  • E-MTAB-10971: scRNA-seq data of the iTracer-perturb (TSC2) organoids

The processed data is available in Mendeley Data: https://doi.org/10.17632/nj3p3pxv6p. The bulk sequencing raw data of barcode and scar libraries are also available in the same Mendeley Data repository.

Contact

If you have any question related to the data and the analysis, please contact Dr. Zhisong He (zhisong.he(at)bsse.ethz.ch), Prof. J. Gray Camp (jarrettgrayson.camp(at)unibas.ch), Prof. Barbara Treutlein (barbara.treutlein(at)bsse.ethz.ch)

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Scripts to analyze iTracer data

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