Notochord and axial progenitors in chicken embryos and human trunk-organoids

This is a repository of scripts used to analyse single-cell transcriptomic data in Rito et al. (2023).

• Data download
• Chicken analyses
• Human analyses
• interspecies comparisons

Data download

The raw sequencing data is publicly available to download at the GEO genomics data repository.

• chicken trunk embryo data (4, 7, 10, 13 somites). Dissociated tissue caudal from 3rd somite.

• human posterior neuruloid data. Day3 micropatterned colonies with several timing delays in BMP&NODAL inhibition.

• human notoroid data. Days 3, 5 and 7 trunk organoids featuring neural, paraxial and axial mesoderm.

Chicken analyses

• Example of read mapping and counting script

• Example QC of a data set

• Analyses

Human analyses

• Example of read mapping and counting script

• QC of individual datasets

• Merge and plot

interspecies comparisons

• RF classifier

Contact regarding analysis/code: Tiago Rito.