Oryza sativa LCM Aya et al, 2011

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Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays.

Aya et al. 2011


Legends:

  1. Gene ID: RAP-japan/IRGSP rice gene locus ID
  2. Cultivar: Nipponbare
  3. Gene data: Derived from supplementary tables ST2-ST25
  4. PO:annotations: best match to the sample description in the following tables. If required the PO annotations to growth stages were done to #both the organ/structure specific development stages and the whole plant growth stages. Every sample has PO whole plant growth stage #annotations.

PO anatomy and growth stage annotations table:

Sample ID Dataset Anatomy PO ID growth stage PO ID growth stage PO ID ' comments
Anther at premeiosis stage, replicate 1_LMD samplePre_antherPO:0009066PO:0001004PO:0007130
Anther_0.3-0.6 mm Anther_0.3-0.6 mmPO:0009066PO:0001004PO:0007130
Anther_0.7-1.0 mm Anther_0.7-1.0 mmPO:0009066PO:0001004PO:0007130
Anther_1.2-1.5 mm Anther_1.2-1.5 mmPO:0009066PO:0001004PO:0007130
Anther_1.6-2.0 mm Anther_1.6-2.0 mmPO:0009066PO:0001004PO:0007130
Embryo_07 DAF Embryo_07 DAF PO:0009009PO:0001095PO:0007042At 5 DAP embryo differentiating the first leaf primordium
Embryo_10 DAF Embryo_10 DAF PO:0009009PO:0001081PO:0007042Morphologically completed 10 DAP embryo
Embryo_14 DAF Embryo_14 DAF PO:0009009PO:0001081PO:0007042milk stage
Embryo_28 DAF Embryo_28 DAF PO:0009009PO:0001081PO:0007010dough
Embryo_42 DAF Embryo_42 DAF PO:0009009PO:0001081PO:0007050
Endosperm_07 DAF Endosperm_07 DAF PO:0009089PO:0007633PO:0007042
Endosperm_10 DAF Endosperm_10 DAF PO:0009089PO:0007633PO:0007042
Endosperm_14 DAF Endosperm_14 DAF PO:0009089PO:0007633PO:0007042
Endosperm_28 DAF Endosperm_28 DAF PO:0009089PO:0007633PO:0007010
Endosperm_42 DAF Endosperm_42 DAF PO:0009089PO:0007633PO:0007050
Inflorescence_0.6-1.0 mm Inflorescence_0.6-1.0 mmPO:0009049 PO:0001083PO:0007006
Inflorescence_3.0-4.0 mm Inflorescence_3.0-4.0 mmPO:0009049 PO:0001083PO:0007006
Inflorescence_5.0-10.0 mm Inflorescence_5.0-10 mmPO:0009049 PO:0001083PO:0007006
Leaf blade_reproductive_00:00 LeafBlade_76DAT_24:00PO:0020039-PO:0007130
Leaf blade_reproductive_12:00 LeafBlade_76DAT_12:00PO:0020039-PO:0007130
Leaf blade_ripening_00:00 LeafBlade_125DAT_24:00PO:0020039-PO:0007010
Leaf blade_ripening_12:00 LeafBlade_125DAT_12:00PO:0020039-PO:0007010
Leaf blade_vegetative_00:00 LeafBlade_27DAT_24:00PO:0020039-PO:0007134
Leaf blade_vegetative_12:00 LeafBlade_27DAT_12:00PO:0020039-PO:0007134
Leaf sheath_reproductive_00:00 LeafSheath_76DAT_24:00PO:0020104-PO:0007130
Leaf sheath_reproductive_12:00 LeafSheath_76DAT_12:00PO:0020104-PO:0007130
Leaf sheath_vegetative_00:00 LeafSheath_27DAT_24:00PO:0020104-PO:0007134
Leaf sheath_vegetative_12:00 LeafSheath_27DAT_12:00PO:0020104-PO:0007134
Lemma_1.5-2.0 mm floret Lemma_1.5-2.0 mm floretPO:0009037PO:0001047PO:0007130
Lemma_4.0-5.0 mm floret Lemma_4.0-5.0 mm floretPO:0009037PO:0001047PO:0007130
Lemma_7.0 mm floret Lemma_7.0 mm floretPO:0009037PO:0001047PO:0007130
Microspore at meiosis stage, replicate 1_LMD sampleMEI-microsporePO:0020048PO:0001009PO:0007130
Microspore at tetrad stage, replicate 1_LMD sampleTET-microsporePO:0000032PO:0001029PO:0007130
Microspore at uninuclear stage, replicate 1_LMD sampleUN-microsporePO:0020048 PO:0001013PO:0007130
Ovary_01 DAF Ovary_01 DAF PO:0009072-PO:0007042
Ovary_03 DAF Ovary_03 DAF PO:0009072-PO:0007042
Ovary_05 DAF Ovary_05 DAF PO:0009072-PO:0007042
Ovary_07 DAF Ovary_07 DAF PO:0009072-PO:0007042
Palea_1.5-2.0 mm floret Palea_1.5-2.0 mm floretPO:0009038 PO:0001048PO:0007130
Palea_4.0-5.0 mm floret Palea_4.0-5.0 mm floretPO:0009038 PO:0001048PO:0007130
Palea_7.0 mm floret Palea_7.0 mm floretPO:0009038 PO:0001048PO:0007130
Pistil_10-14 cm panicle Pistil_10-14 cm inflorescencePO:0009030PO:0007606PO:0007130
Pistil_14-18 cm panicle Pistil_14-18 cm inflorescencePO:0009030PO:0007606PO:0007130
Pistil_5-10 cm panicle Pistil_05-10 cm inflorescencePO:0009030PO:0007606PO:0007130
Pollen at bicelluar stage, replicate 1_LMD sampleBC-pollenPO:0025281PO:0001059PO:0007130
Pollen at tricelluar stage, replicate 1_LMD sampleTC-pollenPO:0025281PO:0001015PO:0007130
Root_reproductive_00:00 Root_76DAT_24:00PO:0009005-PO:0007130
Root_reproductive_12:00 Root_76DAT_12:00PO:0009005-PO:0007130
Root_vegetative_00:00 Root_27DAT_24:00PO:0009005-PO:0007134
Root_vegetative_12:00 Root_27DAT_12:00PO:0009005-PO:0007134
Stem_reproductive_00:00 Stem_83DAT_24:00PO:0009047-PO:0007130
Stem_reproductive_12:00 Stem_83DAT_12:00PO:0009047-PO:0007130
Stem_ripening_00:00 Stem_90DAT_24:00PO:0009047PO:0007010PO:0007010
Stem_ripening_12:00 Stem_90DAT_12:00PO:0009047PO:0007010PO:0007010
Tapetum at meiosis stage, replicate 1_LMD sampleMEI-tapetumPO:0009071 PO:0001009PO:0007130
Tapetum at tetrad stage, replicate 1_LMD sampleTET-tapetumPO:0009071 PO:0001029PO:0007130
Tapetum at uninuclear stage, replicate 1_LMD sampleUN-tapetumPO:0009071 PO:0001013PO:0007130


=====

Table S1 from [Aya et al.http://www.ncbi.nlm.nih.gov/pubmed/22046259] with GEO IDs of the 176 microarray profiles used the study.

GEO_ID DATA SET ID SAMPLE ID CULTIVATOR
GSM534579 LeafBlade_27DAT_12:00_rep1Leaf blade_vegetative_12:00*Nipponbare
GSM534580 LeafBlade_27DAT_12:00_rep2Nipponbare
GSM534581 LeafBlade_27DAT_12:00_rep3Nipponbare
GSM534582 LeafBlade_27DAT_24:00_rep1Leaf blade_vegetative_00:00 Nipponbare
GSM534583 LeafBlade_27DAT_24:00_rep2Nipponbare
GSM534584 LeafBlade_27DAT_24:00_rep3Nipponbare
GSM534585 LeafBlade_76DAT_12:00_rep1Leaf blade_reproductive_12:00 Nipponbare
GSM534586 LeafBlade_76DAT_12:00_rep2Nipponbare
GSM534587 LeafBlade_76DAT_12:00_rep3Nipponbare
GSM534588 LeafBlade_76DAT_24:00_rep1Leaf blade_reproductive_00:00 Nipponbare
GSM534589 LeafBlade_76DAT_24:00_rep2Nipponbare
GSM534590 LeafBlade_76DAT_24:00_rep3Nipponbare
GSM534591 LeafBlade_125DAT_12:00_rep1Leaf blade_ripening_12:00 Nipponbare
GSM534592 LeafBlade_125DAT_12:00_rep2Nipponbare
GSM534593 LeafBlade_125DAT_12:00_rep3Nipponbare
GSM534594 LeafBlade_125DAT_24:00_rep1Leaf blade_ripening_00:00 Nipponbare
GSM534595 LeafBlade_125DAT_24:00_rep2Nipponbare
GSM534596 LeafBlade_125DAT_24:00_rep3Nipponbare
GSM534597 LeafSheath_27DAT_12:00_rep1Leaf sheath_vegetative_12:00* Nipponbare
GSM534598 LeafSheath_27DAT_12:00_rep2Nipponbare
GSM534599 LeafSheath_27DAT_12:00_rep3Nipponbare
GSM534600 LeafSheath_27DAT_24:00_rep1Leaf sheath_vegetative_00:00 Nipponbare
GSM534601 LeafSheath_27DAT_24:00_rep2Nipponbare
GSM534602 LeafSheath_27DAT_24:00_rep3Nipponbare
GSM534603 LeafSheath_76DAT_12:00_rep1Leaf sheath_reproductive_12:00 Nipponbare
GSM534604 LeafSheath_76DAT_12:00_rep2Nipponbare
GSM534605 LeafSheath_76DAT_12:00_rep3Nipponbare
GSM534606 LeafSheath_76DAT_24:00_rep1Leaf sheath_reproductive_00:00 Nipponbare
GSM534607 LeafSheath_76DAT_24:00_rep2Nipponbare
GSM534608 LeafSheath_76DAT_24:00_rep3Nipponbare
GSM534609 Root_27DAT_12:00_rep1Root_vegetative_12:00* Nipponbare
GSM534610 Root_27DAT_12:00_rep2Nipponbare
GSM534611 Root_27DAT_12:00_rep3Nipponbare
GSM534612 Root_27DAT_24:00_rep1Root_vegetative_00:00 Nipponbare
GSM534613 Root_27DAT_24:00_rep2Nipponbare
GSM534614 Root_27DAT_24:00_rep3Nipponbare
GSM534615 Root_76DAT_12:00_rep1Root_reproductive_12:00 Nipponbare
GSM534616 Root_76DAT_12:00_rep2Nipponbare
GSM534617 Root_76DAT_12:00_rep3Nipponbare
GSM534618 Root_76DAT_24:00_rep1Root_reproductive_00:00 Nipponbare
GSM534619 Root_76DAT_24:00_rep2Nipponbare
GSM534620 Root_76DAT_24:00_rep3Nipponbare
GSM534621 Stem_83DAT_12:00_rep1Stem_reproductive_12:00* Nipponbare
GSM534622 Stem_83DAT_12:00_rep2Nipponbare
GSM534623 Stem_83DAT_12:00_rep3Nipponbare
GSM534624 Stem_83DAT_24:00_rep1Stem_reproductive_00:00 Nipponbare
GSM534625 Stem_83DAT_24:00_rep2Nipponbare
GSM534626 Stem_83DAT_24:00_rep3Nipponbare
GSM534627 Stem_90DAT_12:00_rep1Stem_ripening_12:00 Nipponbare
GSM534628 Stem_90DAT_12:00_rep2Nipponbare
GSM534629 Stem_90DAT_12:00_rep3Nipponbare
GSM534630 Stem_90DAT_24:00_rep1Stem_ripening_00:00 Nipponbare
GSM534631 Stem_90DAT_24:00_rep2Nipponbare
GSM534632 Stem_90DAT_24:00_rep3Nipponbare
GSM534633 Inflorescence_0.6-1.0 mm_rep1Inflorescence_0.6-1.0 mm* Nipponbare
GSM534634 Inflorescence_0.6-1.0 mm_rep2Nipponbare
GSM534635 Inflorescence_0.6-1.0 mm_rep3Nipponbare
GSM534636 Inflorescence_3.0-4.0 mm_rep1Inflorescence_3.0-4.0 mm Nipponbare
GSM534637 Inflorescence_3.0-4.0 mm_rep2Nipponbare
GSM534638 Inflorescence_3.0-4.0 mm_rep3Nipponbare
GSM534639 Inflorescence_5.0-10 mm_rep1Inflorescence_5.0-10.0 mm Nipponbare
GSM534640 Inflorescence_5.0-10 mm_rep2Nipponbare
GSM534641 Inflorescence_5.0-10 mm_rep3Nipponbare
GSM534642 Anther_0.3-0.6 mm_rep1Anther_0.3-0.6 mm*Nipponbare
GSM534643 Anther_0.3-0.6 mm_rep2Nipponbare
GSM534644 Anther_0.7-1.0 mm_rep1Anther_0.7-1.0 mm*Nipponbare
GSM534645 Anther_0.7-1.0 mm_rep2Nipponbare
GSM534646 Anther_0.7-1.0 mm_rep3Nipponbare
GSM534647 Anther_1.2-1.5 mm_rep1Anther_1.2-1.5 mm*Nipponbare
GSM534648 Anther_1.2-1.5 mm_rep2Nipponbare
GSM534649 Anther_1.2-1.5 mm_rep3Nipponbare
GSM534650 Anther_1.6-2.0 mm_rep1Anther_1.6-2.0 mm*Nipponbare
GSM534651 Anther_1.6-2.0 mm_rep2Nipponbare
GSM534652 Anther_1.6-2.0 mm_rep3Nipponbare
GSM534653 Pistil_05-10 cm inflorescence_rep1Pistil_5-10 cm panicle*Nipponbare
GSM534654 Pistil_05-10 cm inflorescence_rep2Nipponbare
GSM534655 Pistil_05-10 cm inflorescence_rep3Nipponbare
GSM534656 Pistil_10-14 cm inflorescence_rep1Pistil_10-14 cm panicle Nipponbare
GSM534657 Pistil_10-14 cm inflorescence_rep2Nipponbare
GSM534658 Pistil_10-14 cm inflorescence_rep3Nipponbare
GSM534659 Pistil_14-18 cm inflorescence_rep1Pistil_14-18 cm panicle Nipponbare
GSM534660 Pistil_14-18 cm inflorescence_rep2Nipponbare
GSM534661 Pistil_14-18 cm inflorescence_rep3Nipponbare
GSM534662 Lemma_1.5-2.0 mm floret_rep1Lemma_1.5-2.0 mm floret*Nipponbare
GSM534663 Lemma_1.5-2.0 mm floret_rep2Nipponbare
GSM534664 Lemma_1.5-2.0 mm floret_rep3Nipponbare
GSM534665 Palea_1.5-2.0 mm floret_rep1Palea_1.5-2.0 mm floret*Nipponbare
GSM534666 Palea_1.5-2.0 mm floret_rep2Nipponbare
GSM534667 Palea_1.5-2.0 mm floret_rep3Nipponbare
GSM534668 Lemma_4.0-5.0 mm floret_rep1Lemma_4.0-5.0 mm floret Nipponbare
GSM534669 Lemma_4.0-5.0 mm floret_rep2Nipponbare
GSM534670 Lemma_4.0-5.0 mm floret_rep3Nipponbare
GSM534671 Palea_4.0-5.0 mm floret_rep1Palea_4.0-5.0 mm floret Nipponbare
GSM534672 Palea_4.0-5.0 mm floret_rep2Nipponbare
GSM534673 Palea_4.0-5.0 mm floret_rep3Nipponbare
GSM534674 Lemma_7.0 mm floret_rep1Lemma_7.0 mm floret Nipponbare
GSM534675 Lemma_7.0 mm floret_rep2Nipponbare
GSM534676 Lemma_7.0 mm floret_rep3Nipponbare
GSM534677 Palea_7.0 mm floret_rep1Palea_7.0 mm floret Nipponbare
GSM534678 Palea_7.0 mm floret_rep2Nipponbare
GSM534679 Palea_7.0 mm floret_rep3Nipponbare
GSM534680 Ovary_01 DAF_rep1Ovary_01 DAF* Nipponbare
GSM534681 Ovary_01 DAF_rep2Nipponbare
GSM534682 Ovary_01 DAF_rep3Nipponbare
GSM534683 Ovary_03 DAF_rep1Ovary_03 DAF Nipponbare
GSM534685 Ovary_03 DAF_rep2Nipponbare
GSM534686 Ovary_03 DAF_rep3Nipponbare
GSM534687 Ovary_05 DAF_rep1Ovary_05DAF Nipponbare
GSM534688 Ovary_05 DAF_rep2Nipponbare
GSM534689 Ovary_05 DAF_rep3Nipponbare
GSM534690 Ovary_07 DAF_rep1Ovary_07 DAF Nipponbare
GSM534691 Ovary_07 DAF_rep2Nipponbare
GSM534692 Ovary_07 DAF_rep3Nipponbare
GSM534693 Embryo_07 DAF_rep1Embryo_07 DAF* Nipponbare
GSM534694 Embryo_07 DAF_rep2Nipponbare
GSM534695 Embryo_07 DAF_rep3Nipponbare
GSM534696 Embryo_10 DAF_rep1Embryo_10 DAF Nipponbare
GSM534697 Embryo_10 DAF_rep2Nipponbare
GSM534698 Embryo_10 DAF_rep3Nipponbare
GSM534699 Embryo_14 DAF_rep1Embryo_14 DAF Nipponbare
GSM534700 Embryo_14 DAF_rep2Nipponbare
GSM534701 Embryo_14 DAF_rep3Nipponbare
GSM534702 Embryo_28 DAF_rep1Embryo_28 DAF Nipponbare
GSM534703 Embryo_28 DAF_rep2Nipponbare
GSM534704 Embryo_28 DAF_rep3Nipponbare
GSM534705 Embryo_42 DAF_rep1Embryo_42 DAF Nipponbare
GSM534706 Embryo_42 DAF_rep2Nipponbare
GSM534707 Embryo_42 DAF_rep3Nipponbare
GSM534708 Endosperm_07 DAF_rep1Endosperm_07 DAF* Nipponbare
GSM534709 Endosperm_07 DAF_rep2Nipponbare
GSM534710 Endosperm_07 DAF_rep3Nipponbare
GSM534711 Endosperm_10 DAF_rep1Endosperm_10 DAF Nipponbare
GSM534712 Endosperm_10 DAF_rep2Nipponbare
GSM534713 Endosperm_10 DAF_rep3Nipponbare
GSM534714 Endosperm_14 DAF_rep1Endosperm_14 DAF Nipponbare
GSM534715 Endosperm_14 DAF_rep2Nipponbare
GSM534716 Endosperm_14 DAF_rep3Nipponbare
GSM534717 Endosperm_28 DAF_rep1Endosperm_28 DAF Nipponbare
GSM534718 Endosperm_28 DAF_rep2Nipponbare
GSM534719 Endosperm_28 DAF_rep3Nipponbare
GSM534720 Endosperm_42 DAF_rep1Endosperm_42 DAF Nipponbare
GSM534721 Endosperm_42 DAF_rep2Nipponbare
GSM534722 Endosperm_42 DAF_rep3Nipponbare
GSM722590 Pre_anther_rep1Anther at premeiosis stage, LMD sample*Nipponbare
GSM722591 Pre_anther_rep2Nipponbare
GSM722592 Pre_anther_rep3Nipponbare
GSM722593 MEI-microspore-rep1Microspore at meiosis stage, LMD sample*Nipponbare
GSM722594 MEI-microspore-rep2Nipponbare
GSM722595 MEI-microspore-rep3Nipponbare
GSM722596 MEI-microspore-rep4Nipponbare
GSM722597 TET-microspore-rep1Microspore at tetrad stage, LMD sample*Nipponbare
GSM722598 TET-microspore-rep2Nipponbare
GSM722599 TET-microspore-rep3Nipponbare
GSM722600 UN-microspore-rep1Microspore at uninuclear stage, LMD sample*Nipponbare
GSM722601 UN-microspore-rep2Nipponbare
GSM722602 UN-microspore-rep3Nipponbare
GSM722603 BC-pollen-rep1Pollen at bicelluar stage,LMD sample*Nipponbare
GSM722604 BC-pollen-rep2Nipponbare
GSM722605 BC-pollen-rep3Nipponbare
GSM722606 BC-pollen-rep4Nipponbare
GSM722607 BC-pollen-rep5Nipponbare
GSM722608 BC-pollen-rep6Nipponbare
GSM722609 BC-pollen-rep7Nipponbare
GSM722610 BC-pollen-rep8Nipponbare
GSM722611 TC-pollen-rep1Pollen at tricelluar stage, LMD sample*Nipponbare
GSM722612 TC-pollen-rep2Nipponbare
GSM722613 TC-pollen-rep3Nipponbare
GSM722614 MEI-tapetum-rep1Tapetum at meiosis stage, LMD sample*Nipponbare
GSM722615 MEI-tapetum-rep2Nipponbare
GSM722616 MEI-tapetum-rep3Nipponbare
GSM722617 TET-tapetum-rep1Tapetum at tetrad stage, LMD sample*Nipponbare
GSM722618 TET-tapetum-rep2Nipponbare
GSM722619 TET-tapetum-rep3Nipponbare
GSM722620 UN-tapetum-rep1Tapetum at uninuclear stage, LMD sample*Nipponbare
GSM722621 UN-tapetum-rep2Nipponbare
GSM722622 UN-tapetum-rep3Nipponbare
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IN DISCUSSION