RECOMMENDED README FILE FOR DIGITAL.CSIC DATASETS




GENERAL INFORMATION

1. Title of Dataset: 

Supporting information: Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors 


2. Authors:

Alberto Carbonell, Noah Fahlgren, Skyler Mitchell, Kevin L Cox Jr., Kevin C Reilly, Todd C Mockler, T.C., James C Carrington


3. Date of data collection: N/A


4. Date of data publication on repository: 2024-01


5. Geographic location of data collection <latitude, longitude, or city/region, Country, continent as appropriate>: N/A


6. Information about funding sources that supported the collection of the data (including research project reference/acronym): N/A


7. Recommended citation for this dataset: 

Alberto Carbonell, Noah Fahlgren, Skyler Mitchell, Kevin L Cox Jr., Kevin C Reilly, Todd C Mockler, T.C., James C Carrington (2015). Supporting information: Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors. https://doi.org/10.1111/tpj.12835.



SHARING/ACCESS/CONTEXT INFORMATION

1. Usage Licenses/restrictions placed on the data (please indicate if different data files have different usage license):

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.


2. Links to publications/other research outputs that cite the data: N/A


3. Links to publications/other research outputs that use the data:

Alberto Carbonell, Noah Fahlgren, Skyler Mitchell, Kevin L Cox Jr., Kevin C Reilly, Todd C Mockler, T.C., James C Carrington (2015). Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors. The Plant Journal 82 (6): 1061-1075. doi: 10.1111/tpj.12835 (http://dx.doi.org/10.1111/tpj.12835). 


4. Links to other publicly accessible locations of the data: N/A


5. Links/relationships to ancillary data sets: N/A


6. Was data derived from another source? If so, please add link where such work is located: N/A




DATA & FILE OVERVIEW

1. File List:

Supporting_information.pdf
Data_S1.xlsx
Data_S2.xlsx
Data_S3.xlsx
README.txt


2. Relationship between files, if important: N/A


3. Additional related data collected that was not included in the current data package: N/A


4. Are there multiple versions of the dataset? If so, please indicate where they are located: N/A



METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data:

Figure S1. OsMIR390-B/c vectors for direct cloning of amiRNAs.

Figure S2. Generation of constructs to express amiRNAs from authentic OsMIR390 precursors.

Figure S3. Generation of constructs to express amiRNAs from chimeric OsMIR390-AtL precursors.

Figure S4. Generation of constructs to express amiRNAs from chimeric AtMIR390a-OsL precursors.

Figure S5. Base-pairing of amiRNAs and Brachypodium target mRNAs.

Figure S6. Plant height and seed length analyses in Brachypodium T0 transgenic plants expressing amiR-BdBri1 from authentic OsMIR390 or chimeric OsMIR390-AtL precursors.

Figure S7. Quantification of amiR-BdCao-induced phenotype in Brachypodium 35S:OsMIR390-AtL-Cao, 35S:OsMIR390-Cao and 35S:GUS T0 transgenic lines.

Figure S8. Comparative analyses of the accumulation and processing of several amiRNAs derived from AtMIR390a, AtMIR390a-OsL, OsMIR390 and OsMIR390-AtL precursors in Nicotiana benthamiana leaves.

Figure S9. Base-pairing of amiRNAs and Arabidopsis target transcripts.

Figure S10. Functionality in Arabidopsis T1 transgenic plants of amiRNAs derived from AtMIR390a-based chimeric precursors containing Oryza sativa distal stem-loop sequences (AtMIR390a-OsL).

Figure S11. AmiRNA-induced phenotype quantification in Arabidopsis transgenic plants expressing amiR-AtFt (left) and amiR-AtCh42 (right) from AtMIR390a or chimeric AtMIR390a-OsL precursors.

Figure S12. Target accumulation determined by RNA-Seq analysis in transgenic Brachypodium plants including 35S:OsMIR390-AtL-based or 35S:GUS constructs.

Table S1. MiRbase locus identifiers of Orzya sativa conserved MIRNA precursors.

Table S2. MiRbase locus identifiers of plant MIR390 precursors.

Table S3. AmiRNA phenotypic penetrance in Brachypodium T0 transgenic plants.

Table S4. AmiRNA phenotypic penetrance in Brachypodium T1 transgenic plants.

Table S5. AmiRNA phenotypic penetrance in Arabidopsis T1 transgenic plants.

Table S6. AmiRNA phenotypic penetrance in Arabidopsis T2 transgenic plants.

Table S7. DNA, LNA and RNA oligonucleotides.

Table S8. Sequences and predicted targets for all amiRNAs analyzed.

Table S9. High-throughput small RNA libraries from Arabidopsis, Brachypodium or Nicotiana benthamiana plants.

Table S10. High-throughput strand-specific transcript RNA libraries from independent Brachypodium T0 transgenic lines.

Appendix S1. Characterization of AtMIR390a-OsL-based amiRNAs in eudicots.

Appendix S2. DNA sequence of B/c vectors used for direct cloning of amiRNAs in zero-background vectors containing the OsMIR390 sequence.

Appendix S3. FASTA sequences of all amiRNA-producing MIRNA precursors analyzed.

Appendix S4. Protocol to clone amiRNAs in BsaI/ccdB-based (‘B/c’) vectors including the OsMIR390 precursor.

Data S1A. Differential gene expression analysis between 35S:GUS and 35S:OsMIR390-AtL-Bri1 Brachypodium samples.

Data S1B. Differential gene expression analysis between 35S:GUS and 35S:OsMIR390-AtL-Cad1 Brachypodium samples.

Data S1C. Differential gene expression analysis between 35S:GUS and 35S:OsMIR390-AtL-Cao Brachypodium samples.

Data S1D. Differential gene expression analysis between 35S:GUS and 35S:OsMIR390-AtL-Spl11 Brachypodium samples.

Data S2. Gene counts in RNA-Seq libraries from 35S:GUS, 35S:0sMIR390-AtL-Bri1, 35S:OsMIR390-AtL-Cad1, 35S:0sMIR390-AtL-Cao and 35S:OsMIR390-AtL-Spl11 transgenic Brachypodium lines.

Data S3A. amiR-BdBri1 predicted off-targets differentially underexpressed in 35S:OsMIR390-AtL-Bri1 transgenic Brachypodium plants.

Data S3B. amiR-BdCad1 predicted off-targets differentially underexpressed in 35S:OsMIR390-AtL-Cad1 transgenic Brachypodium plants.

Data S3C. amiR-BdCao predicted off-targets differentially underexpressed in 35S:OsMIR390-AtL-Cao transgenic Brachypodium plants.

Data S3D. amiR-BdSpl11 predicted off-targets differentially underexpressed in 35S:OsMIR390-AtL-Spl11 transgenic Brachypodium plants.



2. Methods for processing the data: N/A


3. Instrument- or software-specific information needed to interpret/reproduce the data, please indicate their location: N/A


4. Standards and calibration information, if appropriate: N/A


5. Environmental/experimental conditions: N/A


6. Describe any quality-assurance procedures performed on the data: N/A


7. People involved with sample collection, processing, analysis and/or submission, please specify using CREDIT roles https://credit.niso.org/: N/A


8. Author contact information: N/A


DATA-SPECIFIC INFORMATION


1. Number of variables: N/A


2. Number of cases/rows: N/A


3. Variable List: N/A


4. Missing data codes: N/A


5. Specialized formats or other abbreviations used: N/A


6. Dictionaries/codebooks used: N/A


7. Controlled vocabularies/ontologies used: N/A