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Alexandre Marand

@marand-lab.bsky.social
197 followers 187 following 33 posts

Assistant Professor at the University of Michigan. Chromatin biology, transcription regulation, plant genomes. marand-lab.github.io

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Reposted by Alexandre Marand
Shawn Cai @xshawncai.bsky.social · 09/10/2026
Have you ever looked at a gene in IGV or a genome browser and wondered “What are all those (ATAC-seq/H3K27ac/CTCF ChIP-seq/…) peaks doing?” 🤔 I’m thrilled to share that we developed a new technology called Swap-seq to answer that exact question. Swap-seq: www.biorxiv.org/content/10.6...
biorxiv.org
Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens
Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to ...
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Reposted by Alexandre Marand
Chenxin Li, PhD @chenxinli2.bsky.social · 07/10/2026
Increase in MYC2 binding sites rather than increase in chromatin accessibility upon JA signaling. #PlantScience From: www.biorxiv.org/content/10.6...
biorxiv.org
Jasmonate-induced expansion of the MYC2 cistrome occurs within a preconfigured chromatin landscape
The transcription factor (TF) MYC2 is a central regulator of jasmonate (JA) signaling, yet its genome-wide occupancy has primarily been characterized using transgenic lines expressing tagged MYC2 prot...
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worm @rfksbrainworm.bsky.social · 02/10/2026
If you ever wondered why visible light is those particular wavelengths, it's because life evolved to see in the narrow range where water is transparent
Diagram of absorption of emf by water. There's a gap right that dips in the 500 nm range
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Reposted by Alexandre Marand
Bas Bargmann @bas-bargmann.bsky.social · 25/09/2026
I am very pleased to present the lab’s first #bluetorial! This concerns our recent publication in Development @dev-journal.bsky.social doi.org/10.1242/dev.... This work, led by postdoc (and former grad student) Kelsey Reed, is the result of many years of hard work by a wonderful team. (1/n)
doi.org
A protoplast-based method to visualize early cell biological events in plant cellular reprogramming and regeneration
Summary: This study presents a live-imaging platform for tracking individual plant protoplasts in culture, enabling analysis of cellular processes, signaling dynamics and developmental transitions.
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fabiogomezcano.bsky.social @fabiogomezcano.bsky.social · 20/09/2026
🚨How many reads in a single-cell barcode come from that cell? 🚨 We loaded maize and Arabidopsis nuclei into separate wells of the same scifi-ATAC plate. Arabidopsis barcode averaged 73% maize reads, yet standard QC looked normal! New preprint 🧵 biorxiv.org/content/10.6... 1/10
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Alexandre Marand @marand-lab.bsky.social · 17/09/2026
🚨New preprint🚨 from super postdoc, @fabiogomezcano.bsky.social, on modeling and removing ambient contamination (i.e. nuclei-free chromatin 🧬) in single-cell scifi-ATAC-seq experiments using his new tool, AmbientMapper. Feedback is welcome! www.biorxiv.org/content/10.6...
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bioRxivpreprint @biorxivpreprint.bsky.social · 17/09/2026
Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping www.biorxiv.org/content/10.64898/20…
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Reposted by Alexandre Marand
Songwen Zhang @songwenz.bsky.social · 16/09/2026
Thrilled to share our new paper in Nature: We found how salicylic acid drives plant immune signaling — it binds its receptor NPR1 and allosterically boosts NPR1’s grip on the Mediator complex (via MED15), switching on defense genes. www.nature.com/articles/s41...
nature.com
Transcriptional activation of plant immunity by salicylic acid - Nature
A mechanistic basis for how the hormone salicylic acid promotes transcriptional activation during plant immune responses is described.
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Reposted by Alexandre Marand
Arvid Herrmann 🍃 @arvidhema.bsky.social · 08/09/2026
Very happy to see this work out as a preprint! 🌽🌱 How are shoot stem cells specified in the maize embryo? We uncover a small RNA-driven morphogenic circuit linking positional information with auxin, cell wall mechanics & cell division patterning. Check it out 👇 www.biorxiv.org/content/10.6...
biorxiv.org
Specification of embryonic shoot stem cells via a small RNA-driven morphogenic circuit
The specification of embryonic stem cells capable of self-renewing and differentiation into virtually any cell type, is one of the most consequential events in the development of a multicellular organ...
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Reposted by Alexandre Marand
Joe Gage @joegage10.bsky.social · 09/09/2026
Ribosomes get stuck in traffic. In plants, where they stall and how tightly they pile up helps decide whether an mRNA gets translated or destroyed. Now out in PNAS, led by @sjorsvdh.bsky.social and Julia Bailey-Serres. www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Reposted by Alexandre Marand
Josh T Cuperus @rnanerd.bsky.social · 07/09/2026
Check out our preprint on Duckweed combo-stress responses and chromatin accessibility. ACRs have ⬆️ GC content much like maize, even with small genomes and low TE numbers. One speculation we had for this in maize was TE insertion avoidance, guess we were wrong. www.biorxiv.org/content/10.6...
biorxiv.org
Duckweeds as Multiplexable Plant Models for Exploring Abiotic Stress Responses
In nature, plants experience complex combinations of environmental stresses. Prior studies using Arabidopsis thaliana show that transcriptional responses to combinatorial stress are unique and cannot ...
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Joe Gage @joegage10.bsky.social · 27/08/2026
New preprint 3 of 3! Happy to have contributed to this one, led by @sjorsvdh.bsky.social: comparing Arabidopsis and maize monosome and disome Ribo-seq shows positional ribosome stalling patterns that are deeply conserved and others that are lineage-specific. www.biorxiv.org/content/10.6...
biorxiv.org
Ribosome stalling position, spacing, and A-site occupancy impact translation and co-translational mRNA decay in plants
Rate limitation in translational elongation causes ribosomes to pause as they decode an open reading frame (ORF). The triggers and outcomes of these events are poorly understood in plants. Here, we si...
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Reposted by Alexandre Marand
Joe Gage @joegage10.bsky.social · 27/08/2026
New preprint 1 of 3! GxE is everywhere, but what causes it at the molecular level? @skdeb.bsky.social led this project using allele-specific expression in a B73xMo17 hybrid to test whether sequence variation changes TF binding & drives cis-reg GxE in gene expression. www.biorxiv.org/content/10.6...
biorxiv.org
Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize
Genotype-by-environment interactions (GxE), or differences in how genotypes perform across varying environments, are a pervasive source of phenotypic variation and underlie differences in local adapta...
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Congratulations to the team @fabiogomezcano.bsky.social, Andrew Luo, and Mark Minow for their enormous effort. We appreciate any feedback or insights the community is willing to offer. 10/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Taken together, we believe cell-specific regulatory mechanisms play a much larger role in heterosis than previously appreciated. Importantly, none of these discoveries would have been possible with single-cell genomics. 9/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Finally, Luguang partioned cell type-resolved ACRs by cis and trans effects. ACRs that lost cell type specificity in hybrids were strongly driven by a combination of cis/trans and trans-only effects, implicating a complex genetic basis to the loss of cellular specificity. 8/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
We also find it interesting that cell-type resolved profiling substantially increased the number of ACRs with non-additive patterns of inheritance. We conclude that bulk tissue methods mask a substantial fraction of dominant and overdominant ACRs. 7/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Next, Luguang looked at inheritance. Although most ACRs are additive, we found that cell-type specificity was strongly correlated with inheritance entropy: in one cross, a ctACR is additive, while overdominant in another. We aren't sure how to explain this yet, insights are welcome!! 6/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Then Luguang found something striking: hybrids had markedly fewer cell-type-specific ACRs. Careful investigation revealed that the cellular breadth of chromatin accessibility is greatly expanded in the hybrid genomes, often by more than 3-fold. We found similar trends in public RNA-seq data. 5/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Interestingly, Luguang found that the distal/proximal partitioning extended to TF motif enrichment: distinct TF families preferenced either proximal or distal ACRs. We find that CPP family TF motifs, regulators of cell proliferation and stress responses, were strongly enriched in distal ACRs. 4/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Gene distal ACRs were strongly associated with sequence and chromatin accessibility variability, and enriched for GWAS hits, consistent with prior publications illustrating distal regulatory regions as catalysts of phenotypic diversity in maize. 3/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
Luguang extensively characterized the haplotype-resolved patterns of chromatin accessibility and sequence identity, revealing disparate conservation between distal and gene-proximal regulatory regions. 2/10
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Alexandre Marand @marand-lab.bsky.social · 26/08/2026
A comprehensive understanding of heterosis has long been out of reach. Led by super postdoc Luguang Jiang, we applied scifi-ATAC-seq to three 🌽 inbred lines and their recip hybrids, and identified a widespread loss of cell-type-specific ACRs in hybrid genomes 🧬 1/10 www.biorxiv.org/content/10.6...
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bioRxivpreprint @biorxivpreprint.bsky.social · 21/08/2026
Cell-type-specific regulatory variation shapes maize heterosis www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 22/07/2026
Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar www.biorxiv.org/content/10.64898/20…
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Reposted by Alexandre Marand
Anders Sejr Hansen @andersshansen.bsky.social · 18/08/2026
Really interesting new paper from Krietenstein and Groth labs showing that FACT depletion has a dramatic effect on microcompartments leading to aberrant microcompartment (AMC) formation through loss of ordered nucleosomes: www.cell.com/molecular-ce...
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Reposted by Alexandre Marand
EPIGENETIC HULK @epigenetichulk.bsky.social · 19/08/2026
HAHAHAHAHAHAHAHAHAHAHAHAHAHA! EPIGENETIC HULK LIKE THIS SMASH! NO SMASH NOTES! www.cell.com/cell-genomic...
cell.com
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting
Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...
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Reposted by Alexandre Marand
Bas Bargmann @bas-bargmann.bsky.social · 11/08/2026
Get yer PR1::RUBY here! www.micropublication.org/journals/bio... Available through Addgene and ABRC (ABRC is still bulking up the seed) www.addgene.org/255430/ abrc.osu.edu/stocks/1211866
micropublication.org
A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation | microPublication
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Brady Lab @bradylabs.bsky.social · 14/08/2026
Our latest preprint! A deep learning framework that maps suberin, lignin and aerenchyma in both monocots and dicots! We present a collection of 1,695 fluorescent images. One surprise-the model works best when trained on both monocots + dicots! www.biorxiv.org/content/10.6...
biorxiv.org
RADIX: a deep learning framework that maps root barriers across species and reveals genetic and environmental contributions
Root anatomical barriers, including the suberized and lignified walls of the endodermis and exodermis, and cortical aerenchyma, regulate water and nutrient transport, gas exchange, and rhizosphere int...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/08/2026
I am excited to announce a job for an Asst Prof in Plant Evolution in the dept. of Evolution and Ecology at @ucdavis.bsky.social. We're looking broadly, from macro (speciation, comparative genomics, evo-devo) to micro (pop biology, adaptive evolution, evo-eco). recruit.ucdavis.edu/JPF07777
recruit.ucdavis.edu
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 11/08/2026
The cellular and genetic basis of inflorescence divergence between maize and teosinte www.biorxiv.org/content/10.64898/20…
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Ian Henderson @hendersi.bsky.social · 25/07/2026
CRISPR-mediated centromere fission generates neochromosomes with distorted meiotic inheritance in Arabidopsis biorxiv.org/content/10.6... new preprint from us - includes changing the Arabidopsis karyotype from 5 -> 6 chromosomes using Cas9 & outcomes of 5/6 chromosome hybrid meiosis
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Joris Sprakel @jorissprakel.bsky.social · 25/07/2026
How do transcription factors bind DNA strongly, and in a switch like manner, while remaining sequence specific? Our new paper on a canonical plant TF suggests the answer is a previously underappreciated assembly state: transcription factor nanoclusters. www.science.org/doi/10.1126/...
science.org
Nanoclustering of a plant transcription factor enables strong yet specific DNA binding
Transcription factor nanoclusters balance the DNA binding trade-off between weakly binding oligomers and nonspecific condensates.
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Brady Lab @bradylabs.bsky.social · 25/07/2026
One of our recent papers describing techniques to identify root barriers to parasitic plant infection. Plus we show that lignin in the cortex can block branched broomrape infection of tomato.
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Adrienne Roeder Lab @roederlab.bsky.social · 10/07/2026
Ever stretch a plastic bag until it wrinkled? Keeping a thin sheet flat while it rapidly expands is surprisingly difficult. So how do growing plant leaves remain flat as they rapidly grow? Check out our new @currentbiology.bsky.social review, How to Grow a Flat Leaf www.cell.com/current-biol...
cell.com
How to grow a flat leaf
Peng et al. review mechanisms driving lamina expansion, including gene expression, auxin-mediated proliferation, and microtubule-directed growth, linking disrupted coordination to morphological defect...
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Michael Raissig @michaelraissig.bsky.social · 08/07/2026
🌾 Every grass leaf shares the same repeating short-long cell pattern in its epidermis. Our new #preprint identifies the protein that builds it. 🔬🧬 📄 preprint: www.biorxiv.org/content/10.6... 🧵⬇️ 1/11
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Michael Raissig @michaelraissig.bsky.social · 04/07/2026
🌾 Grass leaves are the photosynthetic powerhouses of human civilisation. @lbmountain.bsky.social's transcriptomic atlas of nearly 70,000 cells from shoot apex to mature leaf follows the genetic programs that form a grass leaf 🧬 paper doi.org/10.1093/plce... expression browser shiny.ips.unibe.ch
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Min-Yao Jhu @minyaojhu.bsky.social · 24/06/2026
1/ Excited to share our new bioRxiv preprint! "4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs" 📄 doi.org/10.64898/202... Using Xenium, we generated a 4D (3D space + time) atlas of nodule development in Medicago truncatula.
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Sebastián Moreno-Ramírez @sebamorenor.bsky.social · 22/06/2026
Excited to share that our work on single-nucleus RNA-seq of the shoot apical meristem — the shoot stem cell niche — has found a home. #Plantascience #scRNAseq #stemcells www.science.org/doi/10.1126/...
science.org
Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem
snRNA-seq reveals shoot stem cell heterogeneity and traces their differentiation into primary stem cell types.
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Etienne Bucher 🌾🧬🇪🇺 @plantepigenetics.ch · 05/06/2026
We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky
nature.com
An active Helitron transposon family in wheat - Nature Plants
Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...
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José Dinneny @josedinneny.bsky.social · 02/06/2026
So proud to share our latest publication @CellCellPress! Yue Rui reveals that the same enzyme that makes the wall, cellulose synthase complex (CESA), also tethers the plasma membrane to the wall during water-deficit stress, providing resilience. sciencedirect.com/science/articl…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 24/05/2026
Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers www.biorxiv.org/content/10.64898/20…
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Anthony Vecchiarelli @cellforganized.bsky.social · 13/04/2026
New preprint from the Vecchiarelli Lab! 🧵 Congratulations to first author Dr. Claire Dudley! @claire-dudley.bsky.social Claire uncovered a critical player in the organization for the photosynthetic cytoplasm of cyanobacteria - polyphosphate! #polyP www.biorxiv.org/content/10.6...
biorxiv.org
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
This work would not have been possible without the dedicated efforts of all authors. Huge thank you to the @bas-bargmann.bsky.social lab for an awesome collaboration and our funding sources at NIH, NSF, and the USDA. We welcome any suggestions to improve the manuscript.
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
We found that despite the existence of a conserved dedifferentiation program (activated at the onset of dedifferentiation), cell fate transitions are highly heterogeneous. Even when initiated from the same starting cell! What promotes this diversity in reprogramming remains to be discovered.
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
Finally, we applied probabilistic walks to chart reprogramming across the three somatic cell origins and diverse stem cell clusters. This allowed us to identify shared regulatory signatures, quantify dedifferentiation rates, and characterize the role of phytohormones on cell fate outcomes.
Composite figure illustrating probabilistic walks, shared regulatory signatures, dedifferentiation rates, and the generalizable features of dedifferentiation.
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
We also explored how protoplast isolation affects chromatin accessibility. We found that in addition to a widespread increase in accessible chromatin regions (ACRs), several somatic ACRs become condensed. These decommissioned ACRs were exemplified by WRKY TF footprints that became nucleosomal.
Protein foot printing from ATAC data
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
One of the more unexpected finding was expression of LEC2 in cells with mature guard identity, hallmarked by FAMA and SCRM. LEC2 expression was also strongly associated with phytohormone status. We hope to further explore guard cells as a principal source of somatic embryogenesis.
Heatmap and UMAP of LEC2 and stomatal lineage genes
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Alexandre Marand @marand-lab.bsky.social · 23/05/2026
Curiously, epithem-derived stem cells were associated with non-hormone culture. In native tissue contexts, epithem are a major site of auxin biosynthesis. The addition of 2,4-D is likely lethal to these cells and explains why past studies may have missed epithem as a source of totipotency.
Barplot of treatment type enriched partitioned by cell origins. UMAP of auxin biosynthesis gene expression patterns.
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