Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| none | N/A | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| (2E)-4-phenyl-2-[[[3-(trifluoromethyl)phenyl]amino]methylidene]cyclohexane-1,3-dione | Aurora Fine Chemicals | 180.584.762 |
| SULFO-CYANINE5 AZIDE 1MG | LUMIPROBE | A3330 |
| CNQX | Santa Cruz | sc-203003A |
| Gadolinium(III) chloride | Santa Cruz | sc-224004 |
| D(−)-2-Amino-5-phosphonovaleric acid (D-AP5) | Santa Cruz | sc-20043 |
| ABA | Sigma | 862169 |
| Aniline Blue | Sigma | 415049 |
| L-ASCORBIC ACID | Sigma | A4544 |
| 6-Benzylaminopurine | Sigma | B3408 |
| Copper (II) Sulfate | Sigma | 451657 |
| DAPI | Sigma | D9542 |
| 2,4-Dichlorophenoxyacetic acid | Sigma | D7299 |
| L-Glutamic acid potassium salt monohydrate | Sigma | G1501 |
| L-Cysteine (Cys) | Sigma | C7352 |
| L-Serine (Ser) | Sigma | S4311 |
| Inositol | Sigma | I3011 |
| 1-Naphthaleneacetic Acid | Sigma | N0640 |
| Nicotinic acid | Sigma | N0671 |
| Salicylic Acid | Sigma | 247588 |
| Vitamin B1 | Sigma | T4625 |
| Vitamin B6 | Sigma | P5669 |
| ZEATIN | Sigma | Z0164 |
| Critical commercial assays | ||
| Nugen OvationRNA Amplification System V2 | Tecan Genomics | 3100-A01 |
| Nugen Ovation Ultralow DR Multiplex System | Tecan Genomics | 0344NB-08 |
| Deposited data | ||
| Raw and processed ATAC-seq data from root reprogramming cells | This paper | GSE168381 |
| Raw and processed RNA-seq data from root reprogramming cells | This paper | GSE168385 |
| Experimental models: Organisms/strains | ||
| Arabidopsis thaliana Columbia ecotype | ABRC | N/A |
| Arabidopsis thaliana glr1.2 mutant | ABRC | SALK_114822 |
| Arabidopsis thaliana glr3.3–1 mutant | ABRC | SALK_077608 |
| Arabidopsis thaliana glr3.3–2 mutant | ABRC | SALK_082194 |
| Arabidopsis thaliana glr1.2/1.4–1/3.3–1 mutant | Wudick et al., 2018b | N/A |
| Arabidopsis thaliana glr1.2/1.4–1/2.2/3.3–1 mutant | Wudick et al., 2018b | N/A |
| Arabidopsis thaliana glr3.1/3.2/3.3/3.6 mutant | Mou et al., 2020 | N/A |
| Arabidopsis thaliana coi1–2 mutant | Xu et al., 2002 | N/A |
| Arabidopsis thaliana npr1–5 mutant | Zipfel et al., 2004 | N/A |
| Arabidopsis thaliana cbp60g-1 mutant | ABRC | SALK_023199C |
| Arabidopsis thaliana cbp60a-1/cbp60g-1 mutant | ABRC | CS72190 |
| Arabidopsis thaliana npr3–2/npr4–2 mutant | ABRC | CS72351 |
| Arabidopsis thaliana cpk11–2/cpk5/cpk6 mutant | ABRC | CS69906 |
| Arabidopsis thaliana cpk6(a) mutant | ABRC | CS65905 |
| Arabidopsis thaliana cpk6(b) mutant | ABRC | SALK_025460 |
| Zea mays B73 | Jackson Lab CSHL | N/A |
| Zea mays HiII | Jackson Lab CSHL | N/A |
| Oligonucleotides | ||
| Ad1_noMX | Buenrostro, et al., 2013 | AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG |
| Ad2.1_TAAGGCGA | Buenrostro, et al., 2013 | CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT |
| Ad2.2_CGTACTAG | Buenrostro, et al., 2013 | CAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGGAGATGT |
| Ad2.3_AGGCAGAA | Buenrostro, et al., 2013 | CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGGAGATG |
| Ad2.4_TCCTGAGC | Buenrostro, et al., 2015 | CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGGAGATGT |
| Software and algorithms | ||
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| macs2 version 2.1.1 | Zhang et al., 2008 | https://pypi.org/project/MACS2/2.1.1.20160309/ |
| DEseq2 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| HISAT2 | Kim, et al., 2015 | http://daehwankimlab.github.io/hisat2/manual/ |
| Image J software Fiji version 1.52p | Schindelin, et al., 2019 | http://imagej.nih.gov/ij/ |
| VirtualPlant 1.3 | Katari et al., 2010 | http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ |