Reynoso et al. 2019 (PRJNA528488)
General Details
| Title | Multiscale gene expression profiling of 1 cm root tips of control and submerged Oryza sativa, Medicago truncatula, Solanum lycopersicum and Solanum pennellii seedlings |
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| Organism | |
| Number of Samples | 48 |
| Release Date | 2019/03/21 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP189094 |
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| ENA | SRP189094 |
| GEO | GSE128680 |
| BioProject | PRJNA528488 |
Publication
| Title | |
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| Authors | Reynoso MA,Kajala K,Bajic M,West DA,Pauluzzi G,Yao AI,Hatch K,Zumstein K,Woodhouse M,Rodriguez-Medina J,Sinha N,Brady SM,Deal RB,Bailey-Serres J |
| Journal | Science (New York, N.Y.) |
| Publication Date | 2019 Sep 20 |
| Abstract | Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cis motifs and chromatin accessibility associated with submergence up-regulation. Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis motifs, extent of chromatin accessibility, and degree of submergence activation are more prevalent in the wetland crop and may have adaptive importance. Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. |
| PMC | PMC7710369 |
| PMID | 31604238 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR8763884 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq |  |
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| SRR8763886 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763887 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763888 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763889 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763890 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763891 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763892 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763378 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763379 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763380 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763381 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763382 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763383 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763417 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763418 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763419 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763420 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763421 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763422 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763545 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763547 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763548 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763549 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763550 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763551 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763552 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763553 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763609 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763610 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763611 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763612 | PRJNA528488 | Solanum pennellii | Ribo-Seq | |
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| SRR8763613 | PRJNA528488 | Solanum pennellii | Ribo-Seq | |
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| SRR8763614 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763648 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763649 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763650 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763651 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763652 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763653 | PRJNA528488 | Solanum lycopersicum | Ribo-Seq | |
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| SRR8763782 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763784 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763785 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763786 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763787 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763788 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763789 | PRJNA528488 | Medicago truncatula | Ribo-Seq | |
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| SRR8763790 | PRJNA528488 | Oryza sativa | Ribo-Seq | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About