Data from: Conserved gene expression programs in developing roots from diverse plants

Huang L, Schiefelbein J

Date Published: August 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.68686

 

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Title Supplemental DataSet 1
Downloaded 126 times
Description Processed RNA-Seq Gene Expression Values in FPKM. Expression data was obtained from six angiosperm plant species, from three root development zones (MZ, EZ, and DZ), and with three biological replicates each.
Download Supplemental_DataSet1.xlsx (24.20 Mb)
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Title Supplemental DataSet 2
Downloaded 84 times
Description GreenPhyl Defined Gene Families. Genes IDs are included for the seven vascular plants in this study that are present in the 18110 families defined by the GreenPhyl database.
Download Supplemental_DataSet2.xlsx (4.544 Mb)
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Title Supplemental DataSet 3
Downloaded 33 times
Description Distribution of Root-Expressed Genes by Family. The number of root-expressed and non-expressed genes from each plant species in each of the 18110 GreenPhyl defined families. Root expressed genes were defined as those exhibiting FPKM ≥ 0.5 in at least one root development zone, with at least 2 of 3 independent biological replicates generating reads.
Download Supplemental_DataSet3.xlsx (2.704 Mb)
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Title Supplemental DataSet 4
Downloaded 39 times
Description Arabidopsis Genes Preferentially Expressed in Root Developmental Zones. List of Arabidopsis genes preferentially expressed in the meristematic, elongation, and differentiation zones of the primary root. Differential expression analysis was performed by edgeR tag-wise dispersion with upper quartile normalization method (FC ≥ 2 and FDR ≤ 0.05).
Download Supplemental_DataSet4.xlsx (212.1 Kb)
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Title Supplemental DataSet 5
Downloaded 38 times
Description Clustering of Root-Expressed Genes. Temporal gene expression profile types were assigned by fuzzy C-means clustering.
Download Supplemental_DataSet5.xlsx (2.183 Mb)
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Title Supplemental DataSet 6
Downloaded 27 times
Description Supergene Expression in Three Development Zones. The expression in the three zones (meristematic (MZ), elongation (EZ), and differentiation (DZ)) of six angiosperm species and the expression profile types (1 - 9) assigned by fuzzy C-Means clustering are presented for all 18110 GreenPhyl-defined families. Supergene expression was generated by summing all the transcript expressions from the same species within a given family. Type 0 indicated less than 2 fold-change across development zones. NA = no gene present or not root-expressed.
Download Supplemental_DataSet6.xlsx (3.207 Mb)
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Title Supplemental DataSet 7
Downloaded 23 times
Description Supergene Connectivity Values (CNV) for 6161 families possessing root-expressed genes (average FPKM ≥ 0.5 in at least one development zone) from six angiosperm plant species.
Download Supplemental_DataSet7.xlsx (607.7 Kb)
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Title Supplemental DataSet 8
Downloaded 37 times
Description Processed RNA-Seq Gene Expression Values in FPKM. Expression data was generated for seven vascular plant species, two root development zones (meristematic (MZ) and overlapping elongation/differentiation (EDZ)) with three biological replicates each.
Download Supplemental_DataSet8.xlsx (19.26 Mb)
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Title Supplemental DataSet 9
Downloaded 27 times
Description Classification of Genes by Expression Profile. Gene expression fold-change types were assigned to each root-expressed genes from seven vascular plant species.
Download Supplemental_DataSet9.xlsx (14.36 Mb)
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Title Supplemental_DataSet10
Downloaded 22 times
Description Supergene Expression and Profile Types. Supergene expression in two development zones (meristematic (M) and overlapping elongation/differentiation (ED)) of seven vascular species and the expression profile types (1 - 5) assigned by EDZ/MZ fold-change for all 18110 GreenPhyl-defined families.
Download Supplemental_DataSet10.xlsx (2.707 Mb)
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Title Supplemental DataSet 11
Downloaded 14 times
Description Alignment of gene sequences from six angiosperm species. Sequence alignment files are included for each of the phylogenetic trees containing six angiosperm species.
Download Supplemental_DataSet11.zip (227.6 Kb)
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Title Supplemental DataSet 12
Downloaded 19 times
Description Alignment of gene sequences from five plant species. Sequence alignment files are included for each of the phylogenetic trees containing the five plant species.
Download Supplemental_DataSet12.zip (223.0 Kb)
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When using this data, please cite the original publication:

Huang L, Schiefelbein J (2015) Conserved gene expression programs in developing roots from diverse plants. The Plant Cell 27(8): 2119-2132. http://dx.doi.org/10.1105/tpc.15.00328

Additionally, please cite the Dryad data package:

Huang L, Schiefelbein J (2015) Data from: Conserved gene expression programs in developing roots from diverse plants. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.68686
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