OTTR

Supplementary code and data for our manuscript "Organotypic Timelapse recording with Transcriptomic Readout (OTTR) links cell behaviour to cell identity in human tissues" (Vinsland, Mannens et al., manuscript submitted).

 

Figure: OTTR. a) Overview of OTTR's workflow; and b) data modalities acquired.

Preprint (bioRxiv)

https://www.biorxiv.org/content/10.1101/2025.07.28.667119v1

Detailed protocols

https://www.protocols.io/view/ottr-gyydbxxs7

Browser

Visualizations of the dataset will be browsable at CELLxGENE.

Data availability

Raw sequence reads

• scRNA-seq BAM files are available from the European Genome/Phenome Archive (https://ega-archive.org/) under accession number EGAS50000001185.

scRNA-seq expression matrices

• Related to Figure 2 and Extended Data Figure 2

• Complete count matrices (gene ✕ cell counts) for the cultured cortices are available as .loom files:

  cultures_OneMIV_HS.loom (64 MB) - Cultures maintained for One Month in vitro

  cultures_TwoWIV_HS.loom (182 MB) - Cultures maintained for Two Weeks in vitro

  cultures_EYFP.loom (387 MB) - Cultures with lentiviral EYFP expression, cultured for 4 and 11 days in vitro

• The datasets can also be downloaded as .h5ad files from the browser: CELLxGENE.

Xenium spatial data

• Raw Xenium data and images have been deposited at the BioImage Archive under accession number TBA.

• Raw Xenium data and images can also be downloaded directly from here:

  output-XETG00045__0011077__EV37_TL__20231025__135741.gzip (4 GB)

  output-XETG00045__0011077__EV39_con__20231025__135741.gzip (4 GB)

  output-XETG00045__0011080__EV39_TL_A__20231025__135741.gzip (4 GB)

  output-XETG00045__0011080__EV39_TL_B__20231025__135741.gzip (3 GB)

  output-XETG00045__0011080__EV39_TL_C__20231025__135741.gzip (4 GB)

  output-XETG00047__0011072__EV37_con__20231025__140913.gzip (4 GB)

  output-XETG00047__0011075__EV38_TL_A__20231025__140913.gzip (6 GB)

  output-XETG00047__0011075__EV38_TL_B__20231025__140913.gzip (32 GB)

After downloading, Xenium folders can be browsed using the free interactive Xenium Explorer tool.

Timelapse videos

• Supplementary videos:

  Video S1: Cell divisions

  Video S2: Cell accumulation around vessels

  Video S3: Vessel migration

  Video S4: Vessel zoom cell behavior

• Raw timelapse images have been deposited at the BioImage Archive under accession number TBA.

• Cell tracks can be downloaded from here:

  TBD

Code used for analysis and visualisation

scRNA-seq

• Clustering of the scRNA-seq data was performed using the cytograph-dev version of cytograph. This is the version used for our adult human brain project. Its installation and usage are described here.
• Jupyter notebooks used to make figures. The notebooks require cytograph-dev. (NOTE: cytograph-shoji will not work).

Xenium and alignment with timelapse

• Jupyter notebooks to generate the figures can be found here here
• Jupyter notebooks used for Xenium data processing are found [here].
• Notebooks for alignment: