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CARLOS COFRE VEGA
Picture of Soybean obtained from www.pxfuel.com
Project Description
The objective of this project was to analyze Glycine max RNA-seq data sets from different tissues. Differential expression of genes is expected due to the nature of the selected tissues, such as differentiated organs like young and old leaves and non differentiated one, such as shoot apical meristem (SAM). The RNA-seq data was obtained using NGS and analyzed using the HPC from NCSU and the Williams 82 assembly genome was utilized as a reference. More details about the research will be found below.
Biological question
Can gene differential expression be found when analyzing RNA-seq data from different tissues in Glycine max?
Video recording with project explanation
video5047001441.mp4
Reference Genome for this project
Williams 82 ISU01 Assembly v2
Williams 82 ISU01 Assembly v2
Species: Glycine max
Germplasm/cultivar/variety/accession: Williams 82
Version: v2
Why: This assembly is haplotype phased (by sequencing a highly inbred individual of Williams 82), sequenced with PacBio HiFi reads and scaffolded with HiC. It is the most complete soybean assembly.
Publication/website: Haun, W., et al., The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82, Plant Physiology, Volume 155, Issue 2, February 2011, Pages 645–655, https://doi.org/10.1104/pp.110.166736
Note that the publication was for v1 of Williams 82 ISU01. The assembly results and methods described in the publication are for v1. Consult the assembly download page and the JGI release page for information about v2 of this assembly.
Genome assembly download link: https://soybase.org/data/v2/Glycine/max/genomes/Wm82_ISU01.gnm2.JFPQ/glyma.Wm82_ISU01.gnm2.JFPQ.genome_main.fna.gz
Gene annotation: https://soybase.org/data/v2/Glycine/max/annotations/Wm82_ISU01.gnm2.ann1.FGFB/glyma.Wm82_ISU01.gnm2.ann1.FGFB.gene_models_main.gff3.gz
Functional annotation: gff3 doesn't have the functional annotations
About me...
Biotechnology Engineer and Master in Forestry, Universidad de Concepción, Chile.
I worked for 7 years in a Forestry company as a part of the tree breeding program, with high presence in the field (which I love!) before to NCSU pursuing a PhD in Forestry.
Besides being in the wild, I love to play my guitar and play videogames!
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