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Protocols

SoySeq specifications

Information


Unique identifier OMICS_05878
Name SoySeq
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Glycine max

Maintainer


  • person_outline Andrew J Severin

Publication for SoySeq

SoySeq citations

 (12)
library_books

Overexpression of Nictaba Like Lectin Genes from Glycine max Confers Tolerance toward Pseudomonas syringae Infection, Aphid Infestation and Salt Stress in Transgenic Arabidopsis Plants

2016
Front Plant Sci
PMCID: 5078610
PMID: 27826309
DOI: 10.3389/fpls.2016.01590

[…] .ebi.ac.uk/Tools/msa/clustalo/) and EMBOSS Water (http://www.ebi.ac.uk/Tools/psa/emboss_water/), respectively. Normalized RNA-sequencing data was downloaded on the SoyBase website (http://soybase.org/soyseq/) (Severin et al., ). […]

library_books

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA Seq

2015
BMC Biotechnol
PMCID: 4591623
PMID: 26427366
DOI: 10.1186/s12896-015-0207-z

[…] Gene Expression Omnibus [] under accession number [GEO:GSE64620]. Version-controlled data processing and analysis code are available from the project git repository at http://bitbucket.org/lorainelab/soyseq. […]

library_books

Genome wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.)

2015
Front Plant Sci
PMCID: 4585176
PMID: 26442082
DOI: 10.3389/fpls.2015.00773

[…] To acquire the tissue-specific transcript data, the 61 GmHSP70 genes were investigated based on the RNA Seq-Atlas from fourteen tissues (http://soybase.org/soyseq/), including underground tissues (root and nodule), seed development (seed 10-DAF, seed 14-DAF, seed 21-DAF, seed 25-DAF, seed 28-DAF, seed 35-DAF, and seed 42-DAF) and aerial tissues (young le […]

call_split

Genome wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana

2015
J Exp Bot
PMCID: 4526924
PMID: 26188205
DOI: 10.1093/jxb/erv351
call_split See protocol

[…] Transcriptional data for the meta-analysis was collected from publicly available data sets from the Soybean RNA-Seq Atlas (http://www.soybase.org/soyseq/; ); the Soybean eFP Browser (http://bar.utoronto.ca/efpsoybean/cgi-bin/efpWeb.cgi; ); A Common Bean Gene Expression Atlas (http://plantgrn.noble.org/PvGEA/index.jsp; ); and the Arabidopsis eFP […]

library_books

Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily

2014
BMC Plant Biol
PMCID: 4279901
PMID: 25524588
DOI: 10.1186/s12870-014-0373-5

[…] a were introduced to analyze the expression of GmGRAS genes. Data were normalized using a variation of the read s/Kb/Million method, and Z-score analysis was obtained from SoyBase (http://soybase.org/soyseq/). The expression analyses were performed in several organs: young leaf, flower, one-cm pod, pod shell (10 and 14 days after flowering), seed (10, 14, 21, 25, 28, 35, and 42 days after flowerin […]

library_books

Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods

2014
BMC Plant Biol
PMCID: 4263021
PMID: 25430603
DOI: 10.1186/s12870-014-0335-y

[…] ve MMP genes are present in high abundance in flower tissues exposed to elevated [O3], analysis of the expression profiles of the putative MMP genes in soybean using RNA-Seq Atlas (http://soybase.org/soyseq/) found that these genes were not present, or present in low abundance in other soybean tissues. Therefore, it is hypothesized that the increase in abundance of the putative MMP genes identifie […]

Citations

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SoySeq institution(s)
Department of Agronomy, Iowa State University, Ames, IA, USA

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