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

  • [A. thaliana (gene)]
  • Detail of Experiment mapped on Arabidopsis thaliana col Araport11

Details

NameArabidopsis tissue atlas
DescriptionWe used state of the art mass spectrometry and RNA sequencing (RNA-Seq) to provide the first integrated proteomic, phosphoproteomic and transcriptomic atlas of Arabidopsis. For this we measured 30 different Arabidopsis tissues from adult plants, seedlings, callus and cell culture samples to an average depth of 17,603 +/- 1,317 transcripts, 14,430 +/- 911 proteins and 14,689 +/- 2,509 phosphorylation sites. In total we provide protein expression data for 66 % and transcript expression data for 90 % of the annotated protein coding genes (Araport11). For four plant organs we additionally measured consecutive growth stages (rosette leaves, 13 stages; flower, 6 stages; silique, 5 stages; seed, 5 stages).
ContactTechnical University Munich
XrefPRJEB32665
Reference
Conditions55
SpeciesArabidopsis thaliana
Metadata export .CSV   .JSON

Analysis

Mapped Genomes Araport11    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
10d_cellCulture_root Col-0 cell culture root
  • 10d_cellCulture_root_1
  • ERR3333405 
 .bam    .bai    .csi   
14d_callus Col-0 callus plant callus
  • 14d_callus_1
  • 14d_callus_2
  • ERR3333402 
  • ERR3333403 
 .bam    .bai    .csi   
.bam    .bai    .csi   
22d_adult_cotyledon Col-0 adult cotyledon
  • 22d_adult_cotyledon_1
  • ERR3333412 
 .bam    .bai    .csi   
22d_adult_petiole Col-0 adult petiole
  • 22d_adult_petiole_1
  • ERR3333394 
 .bam    .bai    .csi   
22d_adult_root Col-0 adult root
  • 22d_adult_root_1
  • ERR3333396 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf1 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf1_1
  • ERR3333413 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf10 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf10_1
  • ERR3333423 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf11 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf11_1
  • ERR3333424 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf12 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf12_1
  • ERR3333425 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf2 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf2_1
  • ERR3333414 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf3 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf3_1
  • ERR3333415 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf4 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf4_1
  • ERR3333416 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf5 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf5_1
  • ERR3333417 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf6 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf6_1
  • ERR3333418 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf7 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf7_1
  • ERR3333419 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf7_distalPart Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf7_distalPart_1
  • ERR3333392 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf7_proximalPart Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf7_proximalPart_1
  • ERR3333393 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf8 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf8_1
  • ERR3333420 
 .bam    .bai    .csi   
22d_adult_rosetteLeaf9 Col-0 adult rosette leaf
  • 22d_adult_rosetteLeaf9_1
  • ERR3333422 
 .bam    .bai    .csi   
30d_adult_1stNode Col-0 adult stem node
  • 30d_adult_1stNode_1
  • ERR3333389 
 .bam    .bai    .csi   
30d_adult_2ndInternode Col-0 adult stem internode
  • 30d_adult_2ndInternode_1
  • ERR3333390 
 .bam    .bai    .csi   
3d_cellCulture_root Col-0 cell culture root
  • 3d_cellCulture_root_1
  • ERR3333404 
 .bam    .bai    .csi   
7d_seedling_cotyledon Col-0 seedling cotyledon
  • 7d_seedling_cotyledon_1
  • ERR3333406 
 .bam    .bai    .csi   
7d_seedling_hypocotyl Col-0 seedling hypocotyl
  • 7d_seedling_hypocotyl_1
  • ERR3333407 
 .bam    .bai    .csi   
7d_seedling_mixedTissue Col-0 seedling mixed shoot apical meristem, cotyledon and first leaves
  • 7d_seedling_mixedTissue_1
  • ERR3333411 
 .bam    .bai    .csi   
7d_seedling_rootTip Col-0 seedling root tip
  • 7d_seedling_rootTip_1
  • ERR3333408 
 .bam    .bai    .csi   
7d_seedling_upperZone_rootTip Col-0 seedling root tip
  • 7d_seedling_upperZone_rootTip_1
  • ERR3333409 
 .bam    .bai    .csi   
adult_vascular_leaf Col-0 adult adult vascular leaf
  • adult_vascular_leaf_1
  • ERR3333395 
 .bam    .bai    .csi   
carpel Col-0 flower stage 15 carpel
  • carpel_1
  • ERR3333421 
 .bam    .bai    .csi   
cauline_leaf Col-0 adult cauline leaf
  • cauline_leaf_1
  • ERR3333391 
 .bam    .bai    .csi   
drySeedstage_seed Col-0 dry seed stage seed
  • drySeedstage_seed_1
  • ERR3333441 
 .bam    .bai    .csi   
embryoStage10_seed Col-0 embryo stage 10 seed
  • embryoStage10_seed_1
  • ERR3333440 
 .bam    .bai    .csi   
embryoStage6_seed Col-0 embryo stage 6 seed
  • embryoStage6_seed_1
  • ERR3333436 
 .bam    .bai    .csi   
embryoStage7_seed Col-0 embryo stage 7 seed
  • embryoStage7_seed_1
  • ERR3333437 
 .bam    .bai    .csi   
embryoStage8_seed Col-0 embryo stage 8 seed
  • embryoStage8_seed_1
  • ERR3333438 
 .bam    .bai    .csi   
embryoStage9_seed Col-0 embryo stage 9 seed
  • embryoStage9_seed_1
  • ERR3333439 
 .bam    .bai    .csi   
fruit_septum Col-0 adult fruit septum
  • fruit_septum_1
  • ERR3333400 
 .bam    .bai    .csi   
fruit_valve Col-0 adult fruit valve
  • fruit_valve_1
  • ERR3333401 
 .bam    .bai    .csi   
seedImbibitionStage_seed Col-0 seed imbibition stage seed
  • seedImbibitionStage_seed_1
  • ERR3333442 
 .bam    .bai    .csi   
siliqueStage1_silique Col-0 silique stage 1 silique
  • siliqueStage1_silique_1
  • ERR3333431 
 .bam    .bai    .csi   
siliqueStage2_silique Col-0 silique stage 2 silique
  • siliqueStage2_silique_1
  • ERR3333433 
 .bam    .bai    .csi   
siliqueStage3_silique Col-0 silique stage 3 silique
  • siliqueStage3_silique_1
  • ERR3333432 
 .bam    .bai    .csi   
siliqueStage4_silique Col-0 silique stage 4 silique
  • siliqueStage4_silique_1
  • ERR3333434 
 .bam    .bai    .csi   
siliqueStage5_silique Col-0 silique stage 5 silique
  • siliqueStage5_silique_1
  • ERR3333435 
 .bam    .bai    .csi   
stage10_flower Col-0 flower stage 10 flower
  • stage10_flower_1
  • ERR3333427 
 .bam    .bai    .csi   
stage11_flower Col-0 flower stage 11 flower
  • stage11_flower_1
  • ERR3333428 
 .bam    .bai    .csi   
stage12_flower Col-0 flower stage 12 flower
  • stage12_flower_1
  • ERR3333429 
 .bam    .bai    .csi   
stage13_flower Col-0 flower stage 13 flower
  • stage13_flower_1
  • ERR3333430 
 .bam    .bai    .csi   
stage15_flower Col-0 flower stage 15 flower
  • stage15_flower_1
  • ERR3333398 
 .bam    .bai    .csi   
stage15_flowerPedicel Col-0 flower stage 15 flower pedicel
  • stage15_flowerPedicel_1
  • ERR3333397 
 .bam    .bai    .csi   
stage15_petal Col-0 flower stage 15 petal
  • stage15_petal_1
  • ERR3333399 
 .bam    .bai    .csi   
stage15_pollenl Col-0 flower stage 15 pollen
  • stage15_pollenl_1
  • ERR3333443 
 .bam    .bai    .csi   
stage15_sepal Col-0 flower stage 15 sepal
  • stage15_sepal_1
  • ERR3333388 
 .bam    .bai    .csi   
stage15_stamen Col-0 flower stage 15 stamen
  • stage15_stamen_1
  • ERR3333410 
 .bam    .bai    .csi   
stage9_flower Col-0 flower stage 9 flower
  • stage9_flower_1
  • ERR3333426 
 .bam    .bai    .csi