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

[P. trichocarpa (transcript)]
Detail of Experiment mapped on Populus trichocarpa PtV3.1

Details

Name	RNA-seq of major tissues and xylem cell types of Populus trichocarpa
Description	We used the stem cross-sections of P. trichocarpa and our recently developed laser capture microdissection (LCM) to collect fibers, vessels, and a combination of 3 cell types (fibers + vessels + rays). Total RNA from the three samples was isolated, amplified, and analyzed by full-transcriptome RNA-sequencing. The sequencing reads were mapped to the P. trichocarpa genome. Overall design: Different major tissues (shoot tip, leaf, phloem, primary root, stem differentiating xylem) and xylem tissue cell types (fiber, vessel, ray cells) were analyzed by RNA-seq.
Contact	Forest Biotechnology Group, Forestry and Environmental Resources, North Carolina State University
Xref	PRJNA320431
Reference	Shi R et al . 2017;
Conditions	8
Species	Populus trichocarpa
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	PtV3.1
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Genotype	Mutation	Stage	Tissue	Treatment	Level	Time	Samples	Xref	Download alignments
CombinationXylemfiberVesselRaycells			6 months	Xylem	Combination of xylem fiber, vessel and ray cells			CombinationXylemfiberVesselRaycells_1 CombinationXylemfiberVesselRaycells_2 CombinationXylemfiberVesselRaycells_3	SRR3473012 SRR3473013 SRR3473014	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Leaf			6 months	Leaf	Leaf			Leaf_1 Leaf_2 Leaf_3	SRR3472994 SRR3472995 SRR3472996	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Phloem			6 months	Phloem	Phloem			Phloem_1 Phloem_2 Phloem_3	SRR3472997 SRR3472998 SRR3472999	.bam .bai .csi .bam .bai .csi .bam .bai .csi
PrimaryRoot			6 months	Primary root	Primary root			PrimaryRoot_1 PrimaryRoot_2 PrimaryRoot_3	SRR3473000 SRR3473001 SRR3473002	.bam .bai .csi .bam .bai .csi .bam .bai .csi
ShootTip			6 months	Shoot tip	Shoot tip			ShootTip_1 ShootTip_2 ShootTip_3	SRR3472991 SRR3472992 SRR3472993	.bam .bai .csi .bam .bai .csi .bam .bai .csi
StemDifferentiatingXylem			6 months	Stem differentiating xylem	Stem differentiating xylem			StemDifferentiatingXylem_1 StemDifferentiatingXylem_2 StemDifferentiatingXylem_3	SRR3473003 SRR3473004 SRR3473005	.bam .bai .csi .bam .bai .csi .bam .bai .csi
XylemFiberCells			6 months	Xylem	Xylem fiber cells			XylemFiberCells_1 XylemFiberCells_2 XylemFiberCells_3	SRR3473006 SRR3473007 SRR3473008	.bam .bai .csi .bam .bai .csi .bam .bai .csi
XylemVesselCells			6 months	Xylem	Xylem vessel cells			XylemVesselCells_1 XylemVesselCells_2 XylemVesselCells_3	SRR3473009 SRR3473010 SRR3473011	.bam .bai .csi .bam .bai .csi .bam .bai .csi