Data from: Carbonic Anhydrases, EPF2 and a Novel Protease Mediate CO2 Control of Stomatal Development
Biological Repeat 1 - Original files from MISSOU
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Scope And Content | The original BAM and BAI files obtained from the sequencing facility (MISSOU) for the RNA-Seq experiment and the TDF files generated from these BAM and BAI files shown in the original insets of figure 2a (uploaded files include “original” in file names). |
Technical Details | The .zip file contains the original .bam and .bai files which were generated by the sequencing facility at the University of Missouri, Columbia. |
Biological Repeat 1 - Re-analyzed
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Scope And Content | The BAM and BAI and TDF files from this same RNA-seq experiment generated by us using the Tuxedo Suite of programs (TopHat and CuffDiff) with default parameters (aligned to the TAIR 10 annotation) on the GALAXY platform (used for our revised figure 2a; uploaded files include “Re-analyzed” in file names). |
Technical Details | This .zip file contains .bam, .bai, and .tdf files that were generated using the Tuxedo suite of programs (TopHat and CuffDiff) with default parameters (aligned to the TAIR 10 annotation) on the GALAXY platform. |
Biological Repeat 2
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Scope And Content | Data from analyses of the other two independent RNA-seq experiments: BAM, BAI and TDF files for these independent experiments are in components named Biological Repeat 2 and Biological Repeat 3, respectively. |
Technical Details | This .zip file contains .bam, .bai, and .tdf files that were generated using the Tuxedo suite of programs (TopHat and CuffDiff) with default parameters (aligned to the TAIR 10 annotation) on the GALAXY platform. |
Biological Repeat 3
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Scope And Content | Data from analyses of the other two independent RNA-seq experiments: BAM, BAI and TDF files for these independent experiments are in components named Biological Repeat 2 and Biological Repeat 3, respectively. |
Technical Details | This .zip file contains .bam, .bai, and .tdf files that were generated using the Tuxedo suite of programs (TopHat and CuffDiff) with default parameters (aligned to the TAIR 10 annotation) on the GALAXY platform. |
- Collection
- Cite This Work
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Engineer, Cawas B.; Ghassemian, Majid; Anderson, Jeffrey C.; Peck, Scott C.; Hu, Honghong; Schroeder, Julian I. (2015). Data from: Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0TD9V7X
- Description
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Data are deposited here from RNA-Seq transcriptomic experiments analyzing the Arabidopsis response to low and elevated carbon dioxide growing conditions. BAM, BAI and TDF files are uploaded from three independent biological replicates that we conducted for wild type and carbonic anhydrase mutant seedlings. Each set of replicates includes >1000 seedlings per sample and both genotypes were grown at low and elevated CO2 (hence 4 samples per set of replicates). Sampling was done at 5 days after germination to capture early signaling events as seedlings were adapting to the CO2 stimulus.
This project was funded by grants from the National Science Foundation (MCB0918220 and MCB1414339 to J.I.S. and IOS-1025837 to S.C.P.) and the National Institutes of Health (GM060396-ES010337 to J.I.S.), a BAYER-UC Discovery grant (J.I.S.) and a seed grant from the UCSD-SDCSB (GM085764) Systems Biology Center (C.B.E.). A grant from the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy (DE-FG02-03ER15449) to J.I.S. funded complementation and localization analyses. - Date Collected
- 2012 to 2013
- Date Issued
- 2015
- Research Team Head
- Researchers
- Scientific Names
- Topics
- Identifier
- Related Resources
- Engineer, C.B., Ghassemian, M., Anderson, J.C., Peck, S.C., Hu, H., and Schroeder, J.I. (2014) Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development. Nature 513, 246-250. PubMed article: https://www.ncbi.nlm.nih.gov/pubmed/25043023. https://doi.org/10.1038/nature13452
- Raw data at NCBI: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA218542
Primary associated publication
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- License
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Creative Commons Attribution 4.0 International Public License
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- UC Regents
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Under copyright (US)
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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-08-25