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 |