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| Status |
Public on Mar 24, 2021 |
| Title |
Atlas of chromatin accessibility and translatome of tomato and rice root tip cell types |
| Organisms |
Solanum lycopersicum; Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Plant species have evolved specialized cell types and regulatory programs. To understand this diversity, we profiled tomato cell type translatomes and chromatin accessibility. While cell type expression signatures are diverse, some genes exhibit robust cell type expression across time and environments. Using xylem differentiation as a model, newly described, repurposed and conserved genes illustrate this spatial variation. Data integration into regulatory networks demonstrates the function of molecularly uncharacterized cell types. Analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, while other cell types/tissues exhibit species-specific genes and processes. Several transcriptional properties observed in animals were also observed in plants and suggest cross-kingdom higher-order organizational properties. These data serve as a community resource, paving the way for engineering resilient crops.
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| Overall design |
Examination of cell type-specific ATAC and TRAP seq profiles in tomato and rice roots. Tomato plate-based experiments (the nuclear and translating ribosome affinity purification experiments) were conducted with four independent replicates of each of the 12 lines, with T1 seed stocks (and T2 as needed). Tomato pot-based experiments were conducted with four independent replicates of the meristematic cortex and cortex lines and each root tissue was dissected for the lateral roots and the adventitious (hypocotyl-derived) roots. Following filtering steps only four samples were included, one lateral and one adventitious root sample of the meristematic cortex and cortex lines. Tomato field-based experiment was performed with six independent replicates of the meristematic cortex, endodermis, meristematic zone and 35S lines. Following filtering steps, one replicate was removed from the endodermis and one from the meristematic cortex. Rice plate-based experiments were conducted with three independent replicates of the endodermis, vasculature and 35S lines, with T1 seed stocks (and T2 as needed), except for the meristematic cortex for which two independent replicates of two lines were used. Arabidopsis plate-based experiments were done with two independent replicates of the meristematic cortex, endodermis, vasculature and 35S lines as described in Mustroph et al., 2009.
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| Contributor(s) |
Kajala K, Mason GA, Canto-Pastor A, Shaar-Moshe L, Gouran M, Manzano C, Gray S, Kawa D, Yao A, West D, Reynoso M, Pauluzzi G, Sinha N, Bailey-Serres J, Brady S |
| Citation(s) |
34010619 |
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| Submission date |
Apr 23, 2020 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Siobhan Brady |
| E-mail(s) |
sbrady@ucdavis.edu
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| Phone |
5307525183
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| Organization name |
University of California Davis
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| Department |
Genome Center and Plant Biology
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| Lab |
Brady
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| Street address |
451 Health Sciences Dr
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (3) |
| GPL21762 |
Illumina NextSeq 500 (Solanum lycopersicum) |
| GPL21812 |
Illumina HiSeq 4000 (Oryza sativa Japonica Group) |
| GPL25655 |
Illumina HiSeq 4000 (Solanum lycopersicum) |
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| Samples (145)
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| Relations |
| BioProject |
PRJNA627680 |
| SRA |
SRP258125 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149217_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BED, BW) |
| GSE149217_Rice_ATLAS_raw_counts.csv.gz |
964.3 Kb |
(ftp)(http) |
CSV |
| GSE149217_Tomato_ATLAS_raw_counts.csv.gz |
2.0 Mb |
(ftp)(http) |
CSV |
| GSE149217_Tomato_DWL_raw_counts.csv.gz |
548.7 Kb |
(ftp)(http) |
CSV |
| GSE149217_Tomato_Field_raw_counts.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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