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Open Access Highly Accessed Research article

Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq

Chad E Niederhuth123, O Rahul Patharkar123 and John C Walker123*

Author Affiliations

1 Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA

2 Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA

3 Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA

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BMC Genomics 2013, 14:37  doi:10.1186/1471-2164-14-37

Published: 17 January 2013

Additional files

Additional file 1:

Stage 12-17 flowers and dissected receptacles for stages 12-15.

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Additional file 2:

DESeq results. (A) All genes (B) Differentially expressed genes in RNA-Seq with a FDR adjusted p < 0.05 and fold change > 2 fold.

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Additional file 3:

Full GO term-enrichment for RNA-Seq differentially expressed genes.

Format: XLS Size: 81KB Download file

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Additional file 4:

Cluster assignments of differentially expressed genes and microarray mean-normalized expression values used in clustering.

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Additional file 5:

Gap Statistic for different numbers of k-Means clusters.

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Additional file 6:

Full GO term-enrichment for individual clusters. (A) Cluster 1 (B) Cluster 2 (C) Cluster 3.

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Additional file 7:

qPCR across developmental stages 12 (white), 13 (light grey), 14 (dark grey), 15 (black). (A) Wild Type 1 (B)hae hsl2 (C) Wild Type 2 (D)ida. (*) lower than stage 15 (**) higher than stage 15.

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Additional file 8:

(A) Number of genes overlapping between RNA-Seq and Stamen AZ microarrays. (B) Genes overlapping between RNA-Seq and Stamen AZ microarrays. (C) Z-scores of sample overlap between RNA-Seq and Stamen AZ microarrays.

Format: XLS Size: 185KB Download file

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Additional file 9:

Full GO term-enrichment for stage 12-late stage 15 differentially expressed genes that do not overlap with RNA-seq data. (A) Genes showing higher expression from stage 12-late stage 15 (B) Genes showing lower expression from stage 12-late stage 15.

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Additional file 10:

Primer sequences used in qPCR.

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