Arachis Gene Atlas

Arachis hypogaea gene expression: tissue by tissue comparisons
From this table, one can easily obtain the number of differentially expressed genes between any two tissues. There are two corresponding numbers for any tissue pair: The one above the diagonal is the number of genes that have significantly higher expression levels in the tissue presented in the row than that in the column, i.e., tissue-in-row > tissue-in-column. By contrast, the one below the diagonal is the number of genes that have significantly lower expression levels in the tissue presented in the column, i.e., tissue-in-column < tissue-in-row. For instance, in the case comparing lateral stem and main stem leaf, there are 21 genes that have a higher expression in lateral stem than in main stem leaf and there are 23 genes that have a lower expression in lateral stem than in main stem leaf. Clicking on the cell will result in a downloadable list of genes with their DESeq2 analysis results, including mean, log2FoldChange and adjusted-pvalue. In addition, gene GBrowse, sequence link and functional annotation are also included for further exploration.

Raw expression data is available from NCBI's GEO database, accession GSE71357

Credits: Reads were provided by Peggy Ozias-Akins and sequenced by Brian Scheffler and Mary Duke. Samples were harvested and prepared by Ye Chu. Read-mapping and differential expression analysis by Josh Clevenger and Wei Huang.

Citation: A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea.. Josh Paul Clevenger, Ye Chu, Brian Scheffler and Peggy Ozias-Akins. (2016) Frontiers in Plant Biology. Also see associated Arachis hypogaea transcriptome assembly. Data for (GenBank)

Tissues:

• leaf 1::Lateral stem leaf
• leaf 2::Mainstem leaf
• leaf 3::Seedling leaf
• veg shoot::Vegetative shoot tip
• repr shoot::Reproductive shoot tip
• root::Root
• nodule::Nodule
• perianth::Perianth
• stamen::Stamen
• pistil::Pistils
• peg tip 1::Peg tip aerial
• peg tip 2::Peg tip below soil
• peg tip Pat. 1::Peg tip to fruit Pattee 1
• fruit Pat. 1::Fruit Pattee 1
• fruit Pat. 3::Fruit Pattee 3
• pericarp Pat. 5::Pericarp Pattee 5
• pericarp Pat. 6::Pericarp Pattee 6
• seed Pat. 5::Seed Pattee 5
• seed Pat. 6::Seed Pattee 6
• seed Pat. 7::Seed Pattee 7
• seed Pat. 8::Seed Pattee 8
• seed Pat 10::Seed Pattee 10

Numbers in each cell of the following downloadable file are the raw read counts that are uniquely mapped on to Arachis hypogaea genome, produced by HTSeq.

Raw read counts in Arachis hypogaea RNAseq samples

Credits: Reads were provided by Peggy Ozias-Akins and sequenced by Brian Scheffler and Mary Duke. Samples were harvested and prepared by Ye Chu. Read-mapping and differential expression analysis by Josh Clevenger and Wei Huang.

Usage agreement: This analysis is under the same usage agreement (link is external) as for the genome assemblies and annotations. Please contact the authors, or inquire via Contact us, before using or citing this data.