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Sun_et_al_Supplementary_data_re-revised.zip (60.75 MB)

Supplementary data for Sun et al., "Divergence in ABA gene regulatory network underlies differential growth control"

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posted on 2022-03-08, 01:14 authored by Ying Sun, Dong-Ha OhDong-Ha Oh, Lina Duan, Prashanth Ramachandran, Andrea Ramirez, Anna Bartlett, Kieu-Nga TranKieu-Nga Tran, Guannan Wang, Maheshi Dassanayake, José R. Dinneny

Update (Feb. 2nd, 2022): Supplementary data S3 was revised in response to the second peer review, to include gene set enrichment analyses (GSEA) among ABA- and salt-responsive DEG sets.

Update (Sep. 8th, 2021): Supplementary data S1, S4, and S8 were revised in response to peer reviewers' comment, as follows:

- data S1 was revised to include columns indicating orthologs included in AREB/ABF GRN.

- data S4 was revised to include additional worksheets showing full results and selected examples for PiP analyses performed on genes included in AREB/ABF GRN and their ortholog pairs.

- data S8 was revised to include genes in ABA-related pathways, in addition to previous lists of auxin- and ethylene-related pathways.

Currently the zipped archive included both the original and revised data files for reviewing purpose. Upon publication of the manuscript, the archive will have only the final versions.


data S1. All 1-to-1 Orthologous groups with functional genomics data from RNA-seq and DAP-seq.

ABA-responsive gene expression and number of DAP-seq peaks in adjacent genomic regions for 15,198 all unambiguous 1-to-1 ortholog groups.

data S2. An analysis with OrthNet (including duplicates) with functional genomics data from RNA-seq and DAP-seq.

An expanded version of data S1 where all genes, including lineage(s)-specific duplicates and those not in 1-to-1 ortholog groups, organized into OrthNet units based on both sequence similarity and co-linearity. See legend inside the Dataset for details.

data S3. GO enrichment among ABA-induced and repressed DEGs.

A matrix of GO terms enriched in ABA-induced and repressed DEGs for all species, tissues, and time points.

data S4. Phylogenetically informed profiling (PiP) analysis of ABA-responsive gene expression for the four crucifer species.

Results of PiP analysis identifying GO terms showing lineage(s)-specific modifications of ABA-responses. See legend inside the Dataset for details.

data S5. JASPAR motifs enriched among promoters of ABA-induced and repressed DEGs.

A matrix of known transcription factor-binding motifs, obtained from the JASPAR database, enriched in the promoters of ABA-induced and repressed DEGs for all species, tissues, and time points.

data S6. All DAP-Seq peak coordinates with annotations.

All DAP-Seq peak coordinates with number of replicates, types of AREB/ABFs, and other information.

data S7. Conserved ABA GRN.

All genes curated to build the conserved ABA GRN shown in figure 4.

data S8. ABA, Auxin and Ethylene GRN.

All genes curated on the ABA, Auxin and ethylene pathway. 1:1 orthologs identified from RNA-seq and DAP-seq datasets were used to construct the actual GRN.


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