KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
Cellulysin	MilliporeSigma	219466
Pectolyase	MilliporeSigma	P3026
Mannitol	MilliporeSigma	M4125; CAS 69-65-8
MES hydrate	MilliporeSigma	M2933; CAS 1266615-59-1
Murashige and Skoog Basal Medium	MilliporeSigma	M5519
Critical Commercial Assays
Nextera XT DNA Library Preparation Kit	Illumina	FC-131-1024
RNeasy Mini Kit	QIAGEN	74104
TruSeq Stranded mRNA Library Prep Kit	Illumina	20020594
Barcoded dT Beads for Drop-Seq	Macosko et al., 2015; ChemGenes	Lot# 011416B and 072817
Deposited Data
Raw and analyzed Drop-seq and bulk tissue RNA-seq data from Arabidopsis root	This paper	GEO: GSE122687
Cell type-specific microarray data of Arabidopsis root	Brady et al., 2007	N/A (Table S12 of referenced paper)
Cell type-specific RNA-seq data of Arabidopsis root - raw sequence reads	Li et al., 2016	SRA: BioProject PRJNA323955
RNA-seq data of Arabidopsis unopened floral bud tissue	Zhang et al., 2018	GEO: GSM2616967
Experimental Models: Cell Lines
Human HEK293T/17 cells	ATCC	CRL-11268
Mouse embryonic stem cells	Skarnes, 2000	E14Tg2a.4
Experimental Models: Organisms/Strains
Arabidopsis: Col-0	ABRC	CS70000
Arabidopsis: At4CL1p:GFP	Taylor-Teeples et al., 2015	N/A
Arabidopsis: MSL4p:GFP-GUS	Elizabeth Haswell	N/A
Software and Algorithms
Drop-seq_tools v1.12	Macosko et al., 2015	https://github.com/broadinstitute/Drop-seq/releases
Seurat R package (version 2.3.4)	Butler et al., 2018	https://satijalab.org/seurat
Monocle 2 R package (version 2.8.0)	Trapnell et al., 2014	https://bioconductor.org/packages/release/bioc/html/monocle.html
STAR Aligner v2.5.2b	Dobin et al., 2013	https://github.com/alexdobin/STAR
Index of Cell Identity (ICI) algorithm	Efroni et al., 2015	N/A
Other
Resource website and protocol for Drop-seq	Macosko et al., 2015	http://mccarrolllab.org/dropseq