Single-cell mapping of transcriptional and lineage landscape in developing mouse brain

• CREST is a Cre-driven molecular recorder for single cell lineage tracing in vivo.
• CREST reveals a spatiotemporal lineage landscape of developing ventral midbrain.
• Single clonal analysis revealed 7 archetypes of ventral midbrain progenitors with distinct fates.
• Single clonal analysis reveals divergent differentiation routes and corresponding
• transcriptional dynamics of floor plate cells.
• Semi-prospective clonal tracing links transcriptome states of progenitors to their terminal fates across stages.

Preporcess raw single cell RNA data

sh 0.preprocess.sh /R1.fastq /R2.fastq outpath  

CREST Barcode recovering with R package CRESTBuild

Installation

devtools::install_github("Y0NEKO/ChenLab-CREST/CRESTBuild")

Usage:

mycrest = LoadFiles("CREST/data/samplesheet.txt")
thread = 10
mycrest = FindScar(mycrest, thread, match = 1, mismatch = -3, gapOpening = 6, gapExtension = 1)
mycrest = INDELChangeForm(mycrest, thread)
mycrest = INDELCons(mycrest)
write.csv(mycrest@finalIndel, file = "final_scarform.csv", quote = F, row.names = F)

Note: samplesheet.txt is a sample information file contains:reference file(fasta), cutsite, CB_UMI (Please see our example data in "CREST/data").

Please be aware that the current version is under active development. We encourage you to check back regularly for updates and improvements.

License

The CRESTBuild package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation. See the GNU General Public License for more details. A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

other analysis

other analysis method is in BarcodeRecover.R and BarcodeAnalysis.R