Vcl CNCC project

Data and source codes for Vcl CNCC project

R script and code [under Vcl-CNCC-project folder]

• 2021_Wen_Chen_heart_CNCC_integration.html: code for public CNCC single-cell RNA-seq data integration [Figure 5A-E]
• Vcl_CNCC_scRNA-seq_analysis.html: code for our single-cell RNA-seq data analysis [Figure 5F-M]
• Vcl-ST-Seurat-visium.ipynb and Vcl_Spatial_analysis.R: Spatial transcriptome data analysis [Figure 7A-J]

R processed data

Zenodo link https://zenodo.org/record/8251012

Below are the scripts showing the labels of cells in two datasets.

#######################
library(Seurat)

# seurat object for vcl ENCC
print(load("keyRdata/vcl.encc.integrated.Rdata"))

# annotation subtypes in each lineage
table(vcl.combined$lineage.sub)

# condition, normal vs Vcl cKO ENCC
table(vcl.combined$stage)

#######################
# seurat object for vcl CNCC
print(load("E13.5_CNCC_merged_updated.Rdata"))

# sample, ct2 is control and vcl is Vcl cKO CNCC
table(seuset$orig.ident)

# cell annotation file
# unsupervised clusters, see more information in HKU thesis
table(all_tsne$ident)

#######################
# seurat object for public CNCC from E10.5 - P7
print(load("all.cncc.combined.EMBO.mapped.Rdata"))

# annotated cell types based on markers from EMBO paper
table(cncc.combined.sub@active.ident)

# stages of CNCC cells
table(cncc.combined.sub$stage)

Data source (fastq): https://www.embopress.org/doi/full/10.15252/embr.202152389

#######################

spatial data of Vcl (with GFP)

• Vcl-ST-Seurat-visium.ipynb
• data in zenodo database

Raw fastqs in Sequence Read Archive (SRA)

• PRJNAXXXXX (scRNA-seq fastqs)
• PRJNA1004428 (ST raw fastqs)

Contact

• ellyngan engan@hku.hk
• Mingxuan LIANG u3608243@connect.hku.hk
• Zhixin Li zxlee@hku.hk