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. Author manuscript; available in PMC: 2023 Jun 15.
Published in final edited form as: Cell Syst. 2022 Apr 21;13(6):438–453.e5. doi: 10.1016/j.cels.2022.03.006

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Deposited data
scRNA sequencing data - mouse Laukoter et al., 2020 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152716
scRNA sequencing data - human HepG2 Hou et al., 2016 GSM2039769
GSM2039770
HepG2 cell line genome data (Zhou et al., 2019) ENCODE:ENCBS760ISV
GRCm38.p5 NCBI https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.25/
Ensembl EMBL-EBI https://www.ensembl.org/index.html?redirect=no
CA Mouse Genome Project sequencing data Keane et al., 2011 ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz
Supplemental Data

  • Seurat_CountMatrix

  • VCFs

  • HMM_Genotype_Tables

  • Consensus_Trees

  • Dream Challenge

 This study Horwitz, Marshall (2022), “Anderson_LOH_v3”, Mendeley Data, V1, doi: 10.17632/23f7j32zmf.1
Experimental models: organisms/strains
Mouse: CAST/Ei The Jackson Laboratory RRID:IMSR_JAX:000928
Mouse: C57BL/6J The Jackson Laboratory RRID:IMSR_JAX:00066
Mouse:Emx1-Cre The Jackson Laboratory RRID:IMSR_JAX:005628
Software and algorithms
STAR 2.5.0c Dobin et al., 2013 https://github.com/alexdobin/STAR
Seurat R package Butler et al., 2018; Stuart et al., 2019 https://satijalab.org/seurat/
GATK Keane et al., 2011 https://gatk.broadinstitute.org/hc/en-us
HMM R package Prof. Dr. Lin M. Himmelmann, University of Applied Sciences Rapperswil, Switzerland https://cran.r-project.org/web/packages/HMM/index.html
MrBayes Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/
DensiTree Bouckaert, 2010 https://www.cs.auckland.ac.nz/~remco/DensiTree/
Supplemental Code

  • CSI-scRLA Functions.R

  • GEM_SNPCallerGVCF.sh

  • GEM_RGReOrSortSplit.sh

 This study Horwitz, Marshall (2022), “Anderson_LOH_v3”, Mendeley Data, V1, doi: 10.17632/23f7j32zmf.1