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  • SoyBase.org
    Viewer Chromosome SELECT A1 Gm05 A2 Gm08 B1 Gm11 B2 Gm14 C1 Gm04 C2 Gm06 D1a Gm01 D1b Gm02 D2 Gm17 E Gm15 F Gm13 G Gm18 H Gm12 I Gm20 J Gm16 K Gm09 L Gm19 M Gm07 N Gm03 O Gm10 SELECT Gm01 D1a Gm02 D1b Gm03 N Gm04 C1 Gm05 A1 Gm06 C2 Gm07 M Gm08 A2 Gm09 K Gm10 O Gm11 B1 Gm12 H Gm13 F Gm14 B2 Gm15 E Gm16 J Gm17 D2 Gm18 G Gm19 L Gm20 I SoyCyc Search pathway names metabolic reactions compounds and genes are available from SoyCyc Lists of differentially regulated genes with their expression levels can be used in the SoyCyc Omics Viewer to paint reaction steps with colors representing the expression levels of the genes in the list Only genes coding for metabolic enzymes can be visualized in SoyCyc class helptool onclick helpme event this HELP Advanced Metabolism Search 0 window location soycyc SOY substring search type NIL object document getElementById soycycsearchterm value quickSearch Quick Search Search Examples inosine ethanol gibberellin Click Here For The Advanced Metabolism Search Interface Site Map View SoyBase Site Map SoyBase Tutorials Browse SoyBase Tutorials Follow us on Twitter SoyBaseDatabase Take our quick six question survey today SoyBase News RSS Uniform Trial Data now available December 17 2015 An experimental database summarizing the results of the 2012 and 2013 Soybean Uniform Tests Northern Region is available at SoyBase We are making these data available to the community to solicit suggestions for improvements to the data display and functionality of the database These tables are the summary data taken from the Uniform Tests for those years For a full report including methodology and comments see the Northern Test report publications The database could be expanded to include earlier years if there is an interest

    Original URL path: http://soybase.org/ (2016-04-30)
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  • SoyBase - Video Tutorials
    3 onmouseout cleartext 3 How to do a quick BLAST against the soybean genome sequence 1 45 46 Mb MP4 Tutorial describes how to perform an advanced BLAST of an input sequence s against various soybean sequence databases at SoyBase 3 onmouseout cleartext 3 Advanced BLAST analysis at SoyBase 4 07 95 Mb MP4 Tutorial on how to perform a quick search of SoyBase from the home page 3 onmouseout cleartext 3 How to perform a quick search of SoyBase 3 17 79 Mb MP4 Tutorial describing how to quickly determine if an input gene model identifier is involved in a metabolic reaction and what reactions in which it might participate 3 onmouseout cleartext 3 How to perform a SoyCyc quick search 2 01 44 Mb MP4 Tutorial describes how you can quickly get a list of all loci in SoyBase 3 onmouseout cleartext 3 How to quickly get a list of all loci at SoyBase 2 10 80 Mb MP4 Tutorial describes how to get a list of all QTL in SoyBase 3 onmouseout cleartext 3 How do I get a list of all QTL in SoyBase 3 08 79 Mb MP4 Tutorial on how to perform a search of the Fast Neutron mutants using a trait value 3 onmouseout cleartext 3 How to search the Fast Neutron Mutant collection using a trait value 1 51 44 Mb MP4 Tutorial explaining a Fast Neutron Mutant search report 3 onmouseout cleartext 3 Explanation of a Fast Neutron search report 4 07 120 Mb MP4 YouTube Videos of Note Soybean Growth and Development Videos Purdue Extension video describing R6 Full Seed growth stage 4 onmouseout cleartext 4 Soybean Full Seed R6 Growth Stage NDSU Extension video describing soybean growth stages and crop management 4 onmouseout cleartext 4 Soybean Stages Development and Management DuPont Pioneer video describing soybean emergence and planting parameters 4 onmouseout cleartext 4 Understanding Soybean Emergence Univ of Wisconsin Extension video soybean emergence and planting parameters and other factors such as soil compaction and effects on seedlings 4 onmouseout cleartext 4 Soybean Emergence and Germination Common Issues Univ of Wisconsin Extension video on soybean leaf yellowing at V2 stage 4 onmouseout cleartext 4 Soybean Yellowing at V2 growth Purdue Univ Extension video on hail damage to fields at R5 growth stage 4 onmouseout cleartext 4 R5 Soybean Hail Damage Purdue Univ Extension video on hail damage to fields at R4 growth stage 4 onmouseout cleartext 4 R4 Soybean Hail Damage Purdue Univ Extension video describing the later growth stages of soybean R5 R8 4 onmouseout cleartext 4 Later Season Soybean Growth Stages Univ of Wisconsin Extension video describing the growth and development effects of phosphorus and potassium on soybean productivity 4 onmouseout cleartext 4 Potassium Deficiency in Soybean Purdue Univ Extension video describing the affect of potassium difficiency with drought on corn and soybeans 4 onmouseout cleartext 4 Potassium Deficient Corn and Soybean During Drought Tennesse Soybean Promotion Board video on growth staging a field of soybeans 4 onmouseout

    Original URL path: http://soybase.org/tutorials/ (2016-04-30)
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  • SoyBase.org
    plugin such as NoScript add www soybase org to the exclude filter Soybean Genetic Map Information Choose a Linkage Group Linkage Group Chromosome Number A1 5 A2 8 B1 11 B2 14 C1 4 C2 6 D1a 1 D1b 2 D2 17 E 15 F 13 G 18 H 12 I 20 J 16 K 9 L 19 M 7 N 3 O 10 Search SoyBase for Genetic Information SoyBase Search Perform searches of our entire data set Located in the SoyBase Toolbox View or download a list of genetic markers or other features by linkage group Genetic and Sequence Maps Comparison This tool allows a comparison of the genetic and sequence maps After choosing a linkage group chromosome you will see two panes in a CMap display The left pane shows the genetic markers using the order and spacing from the Williams 82 version 1 01 genome assembly The right pane shows the same markers as shown in the Consensus 4 0 genetic map Choose a Linkage Group Linkage Group Chromosome Number A1 5 A2 8 B1 11 B2 14 C1 4 C2 6 D1a 1 D1b 2 D2 17 E 15 F 13 G 18 H 12 I

    Original URL path: http://soybase.org/sbt/ (2016-04-30)
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  • SoyBase Sequence Map Resources Page
    View the JGI Wm82 a2 soybean assembly as pseudomolecules integrating features from the soybean composite genetic and physical maps with the genomic sequence Links from GBrowse features BACs markers to locations in the SoyBase genetic and physical maps are available from a contextual menu The original Wm82 a1 assembly is still available here View or download a list of markers or other sequence map features by chromosomes here Download gene call sequences from the Williams 82 genomic sequence About Genome Nomenclature Convert Version Glyma 1 1 Gene Model Names to Glyma 2 0 Gene Model Names View comparative sequence maps for G max vs 7 wild Glycine species for the NSF SoyMap II project Search for Sequence Features and Annotations SoyBase Search Perform searches of our entire data set See haplotype data for 19 652 cultivars analyzed with the SoySNP50K chip View or download a list of genetic markers or other features by linkage group BARCSOYSSR Potential SSR Database BARCSOYSSR 1 0 a collection of 33 065 potential SSRs identified by Qijian Song and Perry Cregan from the Wm82 genomic sequence has been released These SSRs are now available as a track in the SoyBase Genome Browser The whole dataset

    Original URL path: http://soybase.org/SequenceIntro.php (2016-04-30)
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  • SoyBase.org RNA-Seq Atlas of Glycine max
    in the later Wm82 a1 v1 1 or Wm82 a2 v1 assemblies are not represented in this expression atlas This tool can be used to translate gene model names between all working versions Tissue by Tissue Comparison A table of the significantly differentially expressed genes between any two tissues Gene lists can be downloaded directly from this interactive table Hierarchical Clustering The hierarchical clustering method clusters genes into clades with similar expression profiles Tables and Lists Download raw and normalized data supplementary figures tables and lists Citations Publications RNA Seq Atlas of Glycine max A guide to the soybean transcriptome Andrew J Severin Jenna L Woody Yung Tsi Bolon Bindu Joseph Brian W Diers Andrew D Farmer Gary J Muehlbauer Rex T Nelson David Grant James E Specht Michelle A Graham Steven B Cannon Gregory D May Carroll P Vance and Randy C Shoemaker RNA Seq Atlas of Glycine max A guide to the soybean transcriptome T his RNA Seq atlas extends upon the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and describes new methods that compensate for the increase in transcriptome data obtained from next generation sequencing The RNA Seq Atlas presented here provides high resolution gene expression in a diverse set of fourteen tissues Mining of these data suggests three clades of tissue aerial underground and seed exhibiting transcriptionally similar profiles For example the analysis of the gene expression profiles of over 2 000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that complement or aid in the economically important seed filling process We provide a means for examine genes with differential gene expression between any two tissues The list of genes with a significant increase in gene expression between the tissues can be found

    Original URL path: http://soybase.org/soyseq/ (2016-04-30)
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  • SoyBase.org - Fast Neutron Search
    any of the search functions In addition to providing additional information about the lines derived from the initial mutant the nomenclature is extensible to allow similar names for other mutant types eg transposon insertions EMS treatment etc by replacing the initial letters with ones appropriate to the mutant type Mutant Browsers Browse By Sample Name or Trait Browse By Image Browse By Phenotype Mutant Search Back to top Mutant Description Search Find a specific Sample Load Example 0 var sampval document getElementById sample name value substring 0 document getElementById sample name value indexOf else var sampval document getElementById sample name value window location mutantdetails php mutant escape sampval Search Clear Find all Samples derived from a single M2 plant Load Example Search Clear Find all Samples with specific Trait values Trait Alanine Arginine Ash Aspartic Cysteine Fiber Glutamic Glycine Height Histidine Isoleucine Leucine Linoleic Linolenic Lysine Methionine Moisture Oil Oleic P O Palmitic Phenylalanine Proline Protein Raffinose Sat Fats Serine Stachyose Stearic Sucrose Threonine Tryptophan Tyrosine Valine is 0 document getElementById val value length 0 do search return false Search Reset Use the button to add additional search criteria A range limited search i e 2 x 4 can be accomplished by using the same trait twice where the first uses the operator and the second uses the one Plant Description 0 if document getElementById desc dump childNodes g innerHTML length 0 if g 0 g 0 g g 2 if document getElementById desc dump childNodes g innerHTML length 0 if g 0 g 0 window location filter php descsearch document getElementById desc term value 0 window location filter php descsearch document getElementById desc term value Search Clear View Full Term List Or enter a Plant Ontology or Trait Ontology term Find an Indel by Name 0 window location mutantdetails

    Original URL path: http://soybase.org/mutants/ (2016-04-30)
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  • Analysis Tools
    selective JavaScript blocking plugin such as NoScript add www soybase org to the exclude filter Analysis Tools SoyBase Links Search Glycine max and G soja sequences using BLAST Download Annotations for a Select List of Genes Use the GO Term Enrichment Tool to analyze gene expression changes Convert Version Glyma 1 1 Gene Model Names to Glyma 2 0 Gene Model Names Explore Soybean Metabolic Pathways using SoyBase s SoyCyc

    Original URL path: http://soybase.org/tools.php (2016-04-30)
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  • Community Resources
    as NoScript add www soybase org to the exclude filter Community Resources and Communications Tutorials SoyBase Video Tutorials SoyBase Genetic Map Tutorials SoyBase Sequence Map Tutorials SoyBase Database Searching Tutorials YouTube Videos Soybean Growth and Development Soybean Diseases Soybean Pests Methods and Protocols Making Crosses with Soybean Harvesting Research Plots Community Resources Soybean Breeders Workshop Biennial Conference Molecular Cellular Biology of the Soybean Soybean Genetics Executive Committee membership and history Soybean Genomics Research A Strategic Plan for 2012 2016 A Strategy for Prioritizing Research Goals and Outreach Plans to Reduce Soybean Production Losses Caused by Stink Bugs and Related Insect Pests Job Postings at SoyBase SoyCAP 2005 American Soybean Associataion United Soybean Board North Central Soybean Research Program Soybean Photographs Announcements Tribute to Richard L Bernard August 12 1926 December 20 2012 Communications Soybean Genetics Newsletter USDA Crop and Climatic Resources NASS Crop Progress Report NASS Soybean yield survey 1992 2006 NASS Weekly Weather Summary World Agricultural Outlook Board WAOB Weekly Weather and Crop Bulletin NASS Crop Production Annual Summary NASS Acreage NASS Prospective Plantings Calendar of NASS reports NASS Charts NOAA National Climatic Data Center s North American Drought Monitor Map Germplasm Resources Information Network GRIN Uniform Field and

    Original URL path: http://soybase.org/community_resources.php (2016-04-30)
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