LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

[G. soja (gene)]
Detail of Experiment mapped on Glycine soja W05 GsW05V1

Details

Name	RNA-Seq study reveals genetic responses of diverse wild soybean accessions to increased ozone levels
Description	Analysis of gene expression data from four genetically diverse wild soybean accessions helps reveal both sensitive and resistant responses of the plants to increased ozone levels. Results help characterize genetic response of wild soybean to ozone stress and could help provide information on genetic resources for creating ozone-tolerant soybean breeding lines. Overall design: 2 sensitive genotypes (PI 407179 and PI 424007) and 2 resistant genotypes (PI 424123 and PI 507656) were replicated in 4 complete block designs and subjected to either 75 parts per billion (ppb) ozone or a control of charcoal-filtered conditions (< 10 ppb ozone). Total RNA was isolated from the first three trifoliate of each plant and deep sequenced using Illumina HiSeq 2500.
Contact	Taliercio, Crop Science, NC State University
Xref	PRJNA336336
Reference	Waldeck N et al . 2017;
Conditions	12
Species	Glycine soja
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	GsW05V1
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Genotype	Mutation	Stage	Tissue	Treatment	Level	Time	Samples	Xref	Download alignments
resistant_1stTrifoliate_75ppbOzone	resistant	PI 424123 and PI 507656	first trifoliate	leaf	75 ppb ozone		first trifoliate	resistant_1stTrifoliate_75ppbOzone_1 resistant_1stTrifoliate_75ppbOzone_2 resistant_1stTrifoliate_75ppbOzone_3 resistant_1stTrifoliate_75ppbOzone_4 resistant_1stTrifoliate_75ppbOzone_5 resistant_1stTrifoliate_75ppbOzone_6 resistant_1stTrifoliate_75ppbOzone_7 resistant_1stTrifoliate_75ppbOzone_8	SRR3996496 SRR3996508 SRR3996523 SRR3996535 SRR3996544 SRR3996555 SRR3996570 SRR3996582	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
resistant_1stTrifoliate_Charcoal-filtered	resistant	PI 424123 and PI 507656	first trifoliate	leaf	Charcoal filtered		first trifoliate	resistant_1stTrifoliate_Charcoal-filtered_1 resistant_1stTrifoliate_Charcoal-filtered_2 resistant_1stTrifoliate_Charcoal-filtered_3 resistant_1stTrifoliate_Charcoal-filtered_4 resistant_1stTrifoliate_Charcoal-filtered_5 resistant_1stTrifoliate_Charcoal-filtered_6 resistant_1stTrifoliate_Charcoal-filtered_7	SRR3996490 SRR3996502 SRR3996517 SRR3996529 SRR3996538 SRR3996564 SRR3996576	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
resistant_2ndTrifoliate_75ppbOzone	resistant	PI 424123 and PI 507656	second trifoliate	leaf	75 ppb ozone		second trifoliate	resistant_2ndTrifoliate_75ppbOzone_1 resistant_2ndTrifoliate_75ppbOzone_2 resistant_2ndTrifoliate_75ppbOzone_3 resistant_2ndTrifoliate_75ppbOzone_4 resistant_2ndTrifoliate_75ppbOzone_5 resistant_2ndTrifoliate_75ppbOzone_6 resistant_2ndTrifoliate_75ppbOzone_7 resistant_2ndTrifoliate_75ppbOzone_8	SRR3996497 SRR3996509 SRR3996524 SRR3996536 SRR3996545 SRR3996556 SRR3996571 SRR3996583	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
resistant_2ndTrifoliate_Charcoal-filtered	resistant	PI 424123 and PI 507656	second trifoliate	leaf	Charcoal filtered		second trifoliate	resistant_2ndTrifoliate_Charcoal-filtered_1 resistant_2ndTrifoliate_Charcoal-filtered_2 resistant_2ndTrifoliate_Charcoal-filtered_3 resistant_2ndTrifoliate_Charcoal-filtered_4 resistant_2ndTrifoliate_Charcoal-filtered_5 resistant_2ndTrifoliate_Charcoal-filtered_6 resistant_2ndTrifoliate_Charcoal-filtered_7 resistant_2ndTrifoliate_Charcoal-filtered_8	SRR3996491 SRR3996503 SRR3996518 SRR3996530 SRR3996539 SRR3996550 SRR3996565 SRR3996577	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
resistant_3rdTrifoliate_75ppbOzone	resistant	PI 424123 and PI 507656	third trifoliate	leaf	75 ppb ozone		third trifoliate	resistant_3rdTrifoliate_75ppbOzone_1 resistant_3rdTrifoliate_75ppbOzone_2 resistant_3rdTrifoliate_75ppbOzone_3 resistant_3rdTrifoliate_75ppbOzone_4 resistant_3rdTrifoliate_75ppbOzone_5 resistant_3rdTrifoliate_75ppbOzone_6 resistant_3rdTrifoliate_75ppbOzone_7 resistant_3rdTrifoliate_75ppbOzone_8	SRR3996498 SRR3996510 SRR3996525 SRR3996537 SRR3996546 SRR3996557 SRR3996572 SRR3996584	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
resistant_3rdTrifoliate_Charcoal-filtered	resistant	PI 424123 and PI 507656	third trifoliate	leaf	Charcoal filtered		third trifoliate	resistant_3rdTrifoliate_Charcoal-filtered_1 resistant_3rdTrifoliate_Charcoal-filtered_2 resistant_3rdTrifoliate_Charcoal-filtered_3 resistant_3rdTrifoliate_Charcoal-filtered_4 resistant_3rdTrifoliate_Charcoal-filtered_5 resistant_3rdTrifoliate_Charcoal-filtered_6 resistant_3rdTrifoliate_Charcoal-filtered_7 resistant_3rdTrifoliate_Charcoal-filtered_8	SRR3996492 SRR3996504 SRR3996519 SRR3996531 SRR3996540 SRR3996551 SRR3996566 SRR3996578	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_1stTrifoliate_75ppbOzone	sensitive	PI 407179 and PI 424007	first trifoliate	leaf	75 ppb ozone		first trifoliate	sensitive_1stTrifoliate_75ppbOzone_1 sensitive_1stTrifoliate_75ppbOzone_2 sensitive_1stTrifoliate_75ppbOzone_3 sensitive_1stTrifoliate_75ppbOzone_4 sensitive_1stTrifoliate_75ppbOzone_5 sensitive_1stTrifoliate_75ppbOzone_6 sensitive_1stTrifoliate_75ppbOzone_7 sensitive_1stTrifoliate_75ppbOzone_8	SRR3996499 SRR3996511 SRR3996520 SRR3996532 SRR3996547 SRR3996558 SRR3996567 SRR3996579	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_1stTrifoliate_Charcoal-filtered	sensitive	PI 407179 and PI 424007	first trifoliate	leaf	Charcoal filtered		first trifoliate	sensitive_1stTrifoliate_Charcoal-filtered_1 sensitive_1stTrifoliate_Charcoal-filtered_2 sensitive_1stTrifoliate_Charcoal-filtered_3 sensitive_1stTrifoliate_Charcoal-filtered_4 sensitive_1stTrifoliate_Charcoal-filtered_5 sensitive_1stTrifoliate_Charcoal-filtered_6 sensitive_1stTrifoliate_Charcoal-filtered_7 sensitive_1stTrifoliate_Charcoal-filtered_8	SRR3996493 SRR3996505 SRR3996514 SRR3996526 SRR3996541 SRR3996552 SRR3996561 SRR3996573	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_2ndTrifoliate_75ppbOzone	sensitive	PI 407179 and PI 424007	second trifoliate	leaf	75 ppb ozone		second trifoliate	sensitive_2ndTrifoliate_75ppbOzone_1 sensitive_2ndTrifoliate_75ppbOzone_2 sensitive_2ndTrifoliate_75ppbOzone_3 sensitive_2ndTrifoliate_75ppbOzone_4 sensitive_2ndTrifoliate_75ppbOzone_5 sensitive_2ndTrifoliate_75ppbOzone_6 sensitive_2ndTrifoliate_75ppbOzone_7 sensitive_2ndTrifoliate_75ppbOzone_8	SRR3996500 SRR3996512 SRR3996521 SRR3996533 SRR3996548 SRR3996559 SRR3996568 SRR3996580	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_2ndTrifoliate_Charcoal-filtered	sensitive	PI 407179 and PI 424007	second trifoliate	leaf	Charcoal filtered		second trifoliate	sensitive_2ndTrifoliate_Charcoal-filtered_1 sensitive_2ndTrifoliate_Charcoal-filtered_2 sensitive_2ndTrifoliate_Charcoal-filtered_3 sensitive_2ndTrifoliate_Charcoal-filtered_4 sensitive_2ndTrifoliate_Charcoal-filtered_5 sensitive_2ndTrifoliate_Charcoal-filtered_6 sensitive_2ndTrifoliate_Charcoal-filtered_7 sensitive_2ndTrifoliate_Charcoal-filtered_8	SRR3996494 SRR3996506 SRR3996515 SRR3996527 SRR3996542 SRR3996553 SRR3996562 SRR3996574	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_3rdTrifoliate_75ppbOzone	sensitive	PI 407179 and PI 424007	third trifoliate	leaf	75 ppb ozone		third trifoliate	sensitive_3rdTrifoliate_75ppbOzone_1 sensitive_3rdTrifoliate_75ppbOzone_2 sensitive_3rdTrifoliate_75ppbOzone_3 sensitive_3rdTrifoliate_75ppbOzone_4 sensitive_3rdTrifoliate_75ppbOzone_5 sensitive_3rdTrifoliate_75ppbOzone_6 sensitive_3rdTrifoliate_75ppbOzone_7 sensitive_3rdTrifoliate_75ppbOzone_8	SRR3996501 SRR3996513 SRR3996522 SRR3996534 SRR3996549 SRR3996560 SRR3996569 SRR3996581	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
sensitive_3rdTrifoliate_Charcoal-filtered	sensitive	PI 407179 and PI 424007	third trifoliate	leaf	Charcoal filtered		third trifoliate	sensitive_3rdTrifoliate_Charcoal-filtered_1 sensitive_3rdTrifoliate_Charcoal-filtered_2 sensitive_3rdTrifoliate_Charcoal-filtered_3 sensitive_3rdTrifoliate_Charcoal-filtered_4 sensitive_3rdTrifoliate_Charcoal-filtered_5 sensitive_3rdTrifoliate_Charcoal-filtered_6 sensitive_3rdTrifoliate_Charcoal-filtered_7 sensitive_3rdTrifoliate_Charcoal-filtered_8	SRR3996495 SRR3996507 SRR3996516 SRR3996528 SRR3996543 SRR3996554 SRR3996563 SRR3996575	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi