SGR: Strawberry Genomic Resources
                                                                                                                                           
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  • Home
  • Project description
  • Participating labs
  • Education Activities
  • Bioinf. Workshop
  • Collaborators
  • Publication
  • Genome reannotation
  • RNA-Seq Data Analysis
  • Contacts
  • Item 1a
  • Item 2a
  • Item Folder 3a
    • Sub Item 3.1a
    • Sub Item 3.2a
    • Sub Item 3.3a
    • Sub Item 3.4a
  • Item 4a
  • Item Folder 5a
    • Sub Item 5.1a
    • Item Folder 5.2a
      • Sub Item 5.2.1a
      • Sub Item 5.2.2a
      • Sub Item 5.2.3a
      • Sub Item 5.2.4a
  • Item 6a
  • Samples Info.
  • Differential Expression
    • DEGSeq
    • DESeq
  • Samples Description
  • Gbrowse
  • PO Mapping
  • Search Genes
    • By Gene No.
    • By Gene Desc.
  • Fruit transcriptome analysis
    • Gene Clustering
    • TF Clustering
  • More genomic resources
    • Hormone genes
    • Transcription factors
    • GO assignment
    • Fruit Specific Genes
    • Leaf & Seedling Specific Genes
  • Workshop Info.
  • Parking Directions

The data on this web site are a freely available scientific community resource funded by the National Science Foundation. Please, however, cite the appropriate references (below) when using data or tools from this site for publication. Thank you.

Reference

1) Kang, Darwish, Geretz, Shahan, Alkharouf, and Liu (2013) Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca. Plant Cell; doi:10.1105/tpc.113.111732

2) Darwish, O., Slovin, J. P., Kang, C., Hollender, C. A., Geretz, A., Houston, S., ... & Alkharouf, N. W. (2013). SGR: an online genomic resource for the woodland strawberry. BMC plant biology, 13(1), 223.

3) Hollender C.A., Kang C., Darwish O., Geretz A., Matthews B.F, Slovin J.P., Alkharouf N., Liu Z. (2014) Floral transcriptomes in woodland strawberry uncover developing receptacle and anther gene networks. Plant Physiology 165:1062-1075.

4) Darwish O., Shahan R., Liu Z., Slovin J.P., Alkharouf N. (2015) Re-annotation of the woodland strawberry (Fragaria vesca) genome. BMC Genomics 16:29.

 SampleIDTissueTotal Reads After Filter ? Aligned to genes % Genes Coverage%*
Select1_4flowers_pooledPlant_LCM31087701 24285002 7.5686.75
Select10-11carpel-APlant45391242 37703697 70.0872.13
Select10-11carpel-BPlant32532046 26995535 71.5169.4
Select10carpelsPlant_LCM30395791 23685579 10.2984.38
Select10microsporesPlant_LCM30788482 23878432 5.3986.57
Select12carpel-APlant60705678 50033561 68.6576.86
Select12carpel-BPlant37851326 31191265 68.1274.72
Select6-7receptaclePlant_LCM21997718 14708758 5.7978.2
Select7-8Anther-APlant47403443 40070895 71.274.11
Select7-8Anther-BPlant38488498 32376422 67.2172.86
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* Gene Coverage = Number of genes with at least one read aligned to divided by the total number of genes in the F.Vesca genemark models (34,809).