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. Author manuscript; available in PMC: 2022 Feb 22.
Published in final edited form as: Dev Cell. 2021 Jan 4;56(4):557–568.e6. doi: 10.1016/j.devcel.2020.12.015

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-GFP antibody (GFP-Trap magnetic agarose) ChromoTek Cat#gtma-20; RRID: AB_2631358
Bacterial and Virus Strains
Agrobacterium N/A EHA101
E.coli N/A DH5α
Biological Samples
Zea mays B73 Maize Genetics COOP Stock Center N/A
Zea mays pYAB14-TagRFPt reporter line Je et al., 2016 N/A
Zea mays ZmM16-YFP translational fusion line Bartlett et al., 2015 N/A
Zea mays ZmHDZIV6-YFP translational fusion line This paper N/A
Zea mays CRISPR/Cas9 knock out mutants of ZmVOZs This paper N/A
Zea mays branched silkless1;Tunicate (bd1;Tu) mutants This paper N/A
Chemicals, Peptides, and Recombinant Proteins
Mannitol Sigma-Aldrich Cat# M4125
Bovine serum albumin Sigma-Aldrich Cat#A7907-50G
T7 RNA polymerase Sigma-Aldrich 10881775001
Calcofluor white stain Sigma-Aldrich Cat#18909
Toluidine blue Sigma-Aldrich Cat#T3260
CelLytic™ PN Isolation/Extraction Kit Sigma-Aldrich Cat#CELLYTPN1
Paraformaldehyde Electron Microscopy Sciences Cat#15714-s
Glutaraldehyde Electron Microscopy Sciences Cat#16537-16
Cacodylate buffer Electron Microscopy Sciences Cat#11652
LR white resin Electron Microscopy Sciences Cat#905072
Cellulase RS Onozuka N/A
Cellulase R-10 Onozuka N/A
Macerozyme R-10 Onozuka N/A
Pectolyase Y-23 Duchefa Biochem. Cat#P8OO4.0001
Trypan blue Thermo Fisher Scientific Cat#15250061
Paraplast McCormick Scientific Cat#39503002
ProbeOn Plus™ Slides Fisher Scientific Cat#22-230-900
NBT/BCIP Ready-to-Use Tablets Roche 11697471001
Critical Commercial Assays
Chromium i7 Multiplex Kit 10X Genomics Cat# PN-120262
Chromium Single Cell 3’ Library & Gel Bead Kit v2 10X Genomics Cat#PN-120237
Chromium Single Cell A Chip Kit v2 10X Genomics Cat#PN-1000009
Dynabeads™ MyOne™ Silane Beads Thermo Fisher Scientific Cat#37002D
Arcturus PicoPure RNA Isolation Kit Thermo Fisher Scientific KIT0204
RNA Bioanalyzer kit Agilent Cat#5067-1513
DNA High Sensitivity Bioanalyzer kit Agilent Cat#5067-4626
SMART-Seq™ v4 Ultra™ Low Input RNA Kit Takara Bio USA, Inc. Cat#634890
Nextera XT DNA Library Prep Kit Illumina Cat#FC-131-1024
AMPure XP Beads Beckman Coulter Cat#A63880
KAPA Library Quantification Kits Roche Cat#KK4824
NEXTflex ChIP-seq Kit PerkinElmer Applied Genomics NOVA-5143-02
Deposited Data
B73 whole ear scRNA-seq_replicate 1 This paper PRJNA646989
B73 whole ear scRNA-seq_replicate 2 This paper PRJNA646996
B73 whole ear scRNA-seq_replicate 3 This paper PRJNA647001
Protoplasting-response bulk RNAseq This paper PRJNA647196
pZmYAB14-TagRFPt FACS RNAseq This paper PRJNA647195
pZmYAB14-TagRFPt FACS ATACseq This paper PRJNA647197
ZmHDZIV6-YFP ChIP-seq This paper PRJNA647198
ZmM16-YFP ChIP-seq This paper PRJNA647200
Experimental Models: Cell Lines
N/A N/A N/A
Experimental Models: Organisms/Strains
N/A N/A N/A
Oligonucleotides
See Table S4 for primers or sgRNAs sequences for mRNA in-situ, ZmVOZs crispr and genotyping, ZmHDZIV6-YFP transgene, and bd1 genotyping. N/A N/A
Recombinant DNA
pGW-Cas9 vector Wang et al., 2014 Addgene Plasmid # 50661; RRID: Addgene_50661
pTF101 Gateway-compatible vector Je et al., 2016 NA
Software and Algorithms
STAR Dobin et al., 2013 https://github.com/alexdobin/STAR/wiki
R R Core Team, 2013 https://www.r-project.org/
EmptyDrops Lun et al., 2019 https://rdrr.io/github/MarioniLab/DropletUtils/man/emptyDrops.html
DoubletFinder McGinnis et al., 2019 https://github.com/chris-mcginnis-ucsf/DoubletFinder
Scater McCarthy et al., 2017 https://github.com/Alanocallaghan/scater
Scran Lun et al., 2016 https://github.com/MarioniLab/scran
Rsvd package Erichson et al., 2019 https://github.com/erichson/rSVD
Cccd package Marchette, 2015 https://github.com/cran/cccd
InfoMap Csardi and Nepusz, 2006 https://github.com/mapequation/infomap
MetaNeighbor Crow et al., 2018 https://github.com/maggiecrow/MetaNeighbor
UMAP package Konopka, 2020 https://github.com/tkonopka/umap
EGAD Ballouz et al., 2017 https://github.com/sarbal/EGAD
Trimmomatic - version 0.36 Bolger et al., 2014 http://www.usadellab.org/cms/?page=trimmomatic
edgeR Robinson et al., 2010 https://bioconductor.riken.jp/packages/devel/bioc/html/edgeR.html
elprep Herzeel et al., 2015 https://github.com/ExaScience/elprep
BWA-MEM Li and Durbin, 2009 https://github.com/lh3/bwa
HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/
LDAK software v5.0 Speed et al., 2012 http://www.ldak.org
Other
Cell Strainer pluriStrainer Cat#43-50030-50