Open Access Highly Accessed Research article

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

Andrew J Severin1*, Jenna L Woody1, Yung-Tsi Bolon2, Bindu Joseph1, Brian W Diers3, Andrew D Farmer4, Gary J Muehlbauer6, Rex T Nelson5, David Grant5, James E Specht7, Michelle A Graham15, Steven B Cannon15, Gregory D May4, Carroll P Vance26 and Randy C Shoemaker15

Author Affiliations

1 Department of Agronomy, Iowa State University, Ames, IA 50011, USA

2 United States Department of Agriculture-Agricultural Research Service, Plant Research Unit, St. Paul, MN 55108, USA

3 Department of Crop Sciences, University of Illinois, 1101 West Peabody Dr., Urbana, IL 61801, USA

4 National Center for Genome Resources, Santa Fe, NM 87505, USA

5 United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Resources Unit, Ames, IA 50011, USA

6 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

7 Department of Agronomy, University of Nebraska-Lincoln, Lincoln, NE 68583, USA

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BMC Plant Biology 2010, 10:160  doi:10.1186/1471-2229-10-160

Published: 5 August 2010

Additional files

Additional file 1:

Summary of the RNA-Seq short read sequences. This table includes the number of reads that were of low quality, not mappable to the reference genomes, mapped to the B. Rhizobium genome, highly repetitive (mapped to over 100 locations), repetitive (mapped between 2-100 locations), High quality reads (reads that passed our filtering criteria), unique (mapped to 1 location) and total mappable reads (sum of the highly repetitive and high quality reads).

Format: XLS Size: 43KB Download file

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Additional file 2:

Transcriptionally active genes from all predicted gene models. List of gene models from all the predicted gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.

Format: TXT Size: 673KB Download file

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Additional file 3:

Transcriptionally active genes from the highly-confident gene models. List of gene models from the highly-confident gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.

Format: TXT Size: 574KB Download file

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Additional file 4:

Transcriptionally active genes not from the highly-confident gene models. List of gene models that were transcriptionally active but not part of the list of genes models that are currently considered highly-confident gene models. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model across all tissues was greater than 1.

Format: TXT Size: 98KB Download file

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Additional file 5:

Tissue Specific genes based on Z-score analysis. List of gene models that are that have Z-score value between 3.4 and 3.6 in each tissue.

Format: TXT Size: 117KB Download file

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Additional file 6:

Nodule Specific gene expression. Genes with high gene expression specific to nodule tissue.

Format: XLS Size: 39KB Download file

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Additional file 7:

Seed specific gene expression. Genes with high gene expression specific to seed development.

Format: XLS Size: 56KB Download file

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Additional file 8:

Potential House keeping genes. The top 1000 gene models that showed the lowest coefficient of variance (CV) among all the predicted gene models for all 14 tissues (CV = standard deviation/mean).

Format: CSV Size: 55KB Download file

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Additional file 9:

Housekeeping genes in seed development. Gene list sorted by coefficient of variance for the seven stages in seed development.

Format: CSV Size: 1.4MB Download file

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Additional file 10:

Raw short read sequence count data. Raw short read sequence count data after our filtering criteria (see methods) but before normalization for every predicted gene model in 14 tissues.

Format: CSV Size: 3.1MB Download file

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Additional file 11:

RPKM normalized short read sequence count data. Short read sequence count data after RPKM normalization for every predicted gene model in 14 tissues.

Format: CSV Size: 2.8MB Download file

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Additional file 12:

Genes significantly expressed in underground tissues. List of gene models for which there was as significant change in gene expression in one of the underground tissues (root and nodule) over all other tissues in this study.

Format: CSV Size: 307KB Download file

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Additional file 13:

Genes significantly expressed in seed tissues. List of gene models for which there was as significant change in gene expression in one of the seed tissues (seed 10-DAF, seed 14-DAF, seed 21-DAF, seed 25-DAF, seed 28-DAF, seed 35-DAF and seed 42-DAF) over all other tissues in this study.

Format: CSV Size: 93KB Download file

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Additional file 14:

Genes significantly expressed in aerial tissues. List of gene models for which there was as significant change in gene expression in one of the aerial tissues (young leaf, flower, one cm pod, pod-shell 10-DAF, pod-shell 14-DAF) over all other tissues in this study.

Format: CSV Size: 287KB Download file

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Additional file 15:

Hierarchical clustering of genes significantly expressed in seed tissues. Hierarchical clustering dendrogram of genes with significant expression in seed tissues.

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Additional file 16:

Hierarchical clustering of genes significantly expressed in aerial tissues. Hierarchical clustering dendrogram of genes with significant expression in aerial tissues.

Format: PDF Size: 3.2MB Download file

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Additional file 17:

Hierarchical clustering of genes significantly expressed in underground tissues. Hierarchical clustering dendrogram of genes with significant expression in underground tissues.

Format: PDF Size: 3.3MB Download file

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Additional file 18:

All genes annotated with nutrient reservoir activity. List of gene models from all predicted models that have a GOslim annotation of nutrient reservoir activity.

Format: TXT Size: 2KB Download file

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Additional file 19:

Genes annotated with nutrient reservoir activity expressed in seed development. Table of gene models with a GOslim annotation of nutrient reservoir activity found in seed development and their possible function based on their homologous Dana Farber tentative consensus sequence.

Format: XLS Size: 40KB Download file

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Additional file 20:

All genes annotated with lipoxygenase activity. List of gene models from all predicted models that have a GOslim annotation of lipoxygenase activity.

Format: TXT Size: 1KB Download file

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Additional file 21:

Interval matching script. Script to perform interval matching of short read sequence intervals after lignment with GSNAP and predicted gene models (Glyma1.01 genome assembly).

Format: R Size: 4KB Download file

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Additional file 22:

Heatmap of highest expressed genes. This figure is the actual output from the heatmap.2 R command. Each cell in heatmap for the highest expressed genes contains the name of the gene model.

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Additional file 23:

Heatmap of legume specific genes. This figure is the actual output from the heatmap.2 R command. Each cell in the heatmap for the legume specific genes contains the name of the gene model.

Format: PDF Size: 1.8MB Download file

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