ArrayExpressapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-4372/E-MTAB-4372.sdrf.txtftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-4372/E-MTAB-4372.idf.txtprimaryOK20000370TranscriptomicsXu ChunmingIllumina Genome Analyzer IIxOryza Sativa Japonica Grouphttps://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4372RNA-seq of coding RNAchunmingnenu@163.comArrayExpressLibrary Construction - 6 µg of total RNA was used to construct random oligo dT libraries using Illumina TrueSeq RNA sample Preparation kit (GATC, Switzerland).
Sequencing - Illumina Genome Analyzer IIx370Rice (Oryza sativa) is a staple crop that supports half the world's population and an important monocot model system. Monocot leaf matures in a basipetal manner, and has a well-defined developmental gradient along the longitudinal axis. However, little is known about its transcriptional dynamics after leaf maturation. In this study, we have reconstructed a high spatial resolution transcriptome for the matured rice leaf by sectioning the leaf into seven 3-cm fragments. We have performed strand-specific Illumina sequencing to generate gene expression profiles for each fragment. We found that the matured leaf contains a longitudinal gene expression gradient, with 6.97% (2,603) of the expressed genes showing differentially expression along the seven sections. The leaf transcriptome showed a gradual transition from accumulating transcripts related to primary cell wall and basic cellular metabolism at the base to those involved in photosynthesis and energy production in the middle, and catabolic metabolism process toward the tip.Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf.Li Ning N, Chen Yun-Ru YR, Ding Zehong Z, Li Pinghua P, Wu Ying Y, Zhang Ai A, Yu Sheng S, Giovannoni James J JJ, Fei Zhangjun Z, Zhang Wei W, Xiang Jenny Z JZ, Xu Chunming C, Liu Bao B, Zhong Silin Sproto-oncogene c-Kit, RNA, Ribonucleic, Illumina Genome Analyzer IIx., total RNA extract, ribose nucleic acid, ribonucleic acids, SCF receptor activity, Illumina GA IIx, RGD1309698, Tr-kit, RNS, Xkl-1, PBT, KL receptor activity, Gsfsco1, scfr, KIT ligand receptor activity, yeast nucleic acid, Ribonukleinsaeure, Gene Products, SCO5, kl1-A, pentosenucleic acids, Ribonucleic acids, SCO1, KIT, Gsfsow3, SCFR, Gsfsco5, Library, Non Polyadenylated, RNA Gene Products, XKrk1, SOW3, Random selection by shearing, tyrosine-protein kinase Kit, ribonucleic acid, Acid, oligonucleotide random primer, pbt, c-KIT, Fdc, library construction, 2010003O18Rik, Non Polyadenylated RNA, Non-Polyadenylated, nucleic acid library construction, nucleic acid library preparation, Ribonucleic Acid, kit, W, CD117, 15E1.2, Non-Polyadenylated RNA, c-kit, RANDOM, C-Kit, Ssm, xkl-1, Bs, Sl, krk1red rice, RNA-seq, exact)., transcription profiling by high throughput sequencing, exact), Asian cultivated rice, rice, hoja (Spanish, 葉 (Japanesebig, Plant Sprout, Nup32D, PLIP, l(1)VE614, STRAA1, RNA Sequence Determination, Transcriptome Profile, Strra1, Sequence Determination, RNA Sequence, AA959952, Gene Expression Profile, Gene, l(2)02029, Profiles, brl, Type 2A-interacting protein, ESA1, SCARA1, Cut, large, DmelCG4114, exact), l(1)7Ba, l(1)7Bb, dJ69E11.3, CYFIP1/2, Arabidopsis NAC domain containing protein 91, Sprouted Seed, CG6072, zk, Sra-1/CYFIP, Malted, Analysis, HTATIP, nup154, anon-WO0118547.92, Vasp, study, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, l(2)10432, Malted Grain, Grain, Analyses, Determination, nebula, Profile, N, Tissue, CG4931, Straa1, Sequence Determinations, kf, Signatures, Sequencing, CG11387, VASP, 89B, nla, ms(2)zk, DmelCG4579, DmelCG11387, cPLA2, RNA Sequence Analyses, Expression Signature, anon-WO0172774.10, great, sample, CYFIP, Sprouted, MENA, Transcriptomes, CT, 89B11, RNA Sequencing, liquid, l(2)01501, SR-A, Viewpoint, Editorial Comment, pp7684, TIP, DmelCG6072, CD204, Asian cultivated rice, Sequence Analyses, RNA, Transcriptome, Sra1, Data Set, Malted Grains, RNA Sequence Determinations, ZC2HC5, BcDNA:LD21772, PIR121/Sra-1, sra-1, Expression Profiles, Oryza sativa Nipponbare, CG4114, Ct, HTATIP1, tip, Sprout, ANAC091, Oryza sativa cultivar Nipponbare, Expanded, Determinations, Commentary, whole transcriptome, l(3)05203, Gene Expression, Sra1/PIR121, Putative MAPK-activating protein PM10, Plant Sprouts, Stickstoff, Expression Signatures, 1270, Gene Expression Signatures, red rice, Gene Expression Signature, Seed, BcDNA:GH10590, TIP60, Enb, Nipponbare, PIR121, ENA, Ena, Expression Profile, sra1, CG15112, Transcriptome Profiles, ENA/VASP, Seeds, Sra, SRA, Sprouts, nup32D, Srap, NDPP1, Oryza sativa, expanded, Plant, CG4579, Ex, azote, enb, hoja (Spanish, 葉 (Japanese, sample population, nitrogeno, l(2)01270, incised, phSR1, phSR2, Seedling, sample., Grains, red rice <Oryza sativa>, DmelCG4931, nitrogen, SRAP, enlarged, Gene Expression Profiles, rice, RNA Sequence Analysis, Sprouted Seeds, TCV-interacting protein, dSra, l(2)ey, DSra-1, Signature, 7N, tlp, TIP41, FE65L2biochemical pathways, projections, Nup32D, Ghrfr, Metabolic Process, PLIP, Materials, Nucleotide Sequencing, second cervical vertebra, Massively-Parallel, Metabolic Concepts, LUC7A, Gene Expression Profile, Profiles, Type 2A-interacting protein, Photosynthetic Carbon Fixation, axis vertebra, School-Age, High-Throughput RNA Sequencing, exact), dJ69E11.3, Concepts, Metabolism Concept, Phenomenon, Carbon Fixation, HTATIP, Deep Sequencing, Gene Expressions, Illumina Sequencing, catabolism, C2, bases, Basen, metabolic process resulting in cell growth, Calvin-Benson-Bassham, Signatures, reaction, High Throughput RNA Sequencing, cPLA2, vertebra 2, Expression Signature, papilla, intermediary metabolism, Transcriptomes, biotransformation, nup154., Calvin, Catabolism, TIP, Asian cultivated rice, High-Throughput RNA, anatomical protrusion, Process, Nucleobase, ZC2HC5, CROP, metabolism resulting in cell growth, Crop, Expression Profiles, lamina, High-Throughput DNA Sequencing, flanges, C2 vertebra, lit, Calvin Benson Cycle, HTATIP1, tip, ANAC091, Gene Expression, Putative MAPK-activating protein PM10, Ion Torrent Sequencing, School Age, Expression Signatures, Massively-Parallel Sequencing, Base2, Base1, shelf, red rice, Next-Generation, Genetic Materials, secretion, Ion Torrent, TIP60, Expression Profile, Genetic Material, little, Transcriptome Profiles, Populations, craw, shelves, CREAP-1, Calvin Benson Bassham Cycle, axis [C II], projection, 葉 (Japanese, ridge, organ system, High Throughput Sequencing, Material, spine, rice, Base, Cistron, School-Age Population, tlp, TIP41, base, hLuc7A, High Throughput DNA Sequencing, Transcriptome Profile, Processes, lamellae, Gene, stalk, High-Throughput DNA, Reductive Pentose Phosphate Cycle, Metabolic Processes, body system, process of organ, Illumina, Next-Generation Sequencing, ESA1, protrusion, lamella, Deep, Metabolism, Arabidopsis NAC domain containing protein 91, Photosynthesis Dark Reactions, Cycle, zk, system, Massively Parallel Sequencing, Metabolism Phenomena, RGD1307981, School-Age Populations, study, l(2)10432, anatomical systems, Ion Proton Sequencing, Genetic, Profile, axis (CII), Metabolic Concept, Pyrosequencing, ridges, Population, Expressions, culm, Sequencing, ms(2)zk, DmelCG4579, High-Throughput, RNA Sequencing, Calvin-Benson-Bassham Cycle, Expression, l(2)01501, School Age Population, Dark Reactions of Photosynthesis, laminae, Transcriptome, degradation, axis, Photosynthetic, anatomical process, BcDNA:LD21772, OA48-18, Photosynthesis Dark Reaction, Cistrons, Concept, Metabolic Phenomena, whole transcriptome, Metabolism Concepts, cervical axis, DNA Sequencing, Gene Expression Signatures, Phenomena, CRA, Calvin-Benson Cycle, Gene Expression Signature, connected anatomical system, metabolism, flange, organ process, Next Generation Sequencing, Metabolic Phenomenon, multicellular organism metabolic process, nup32D, biodegradation, Metabolic, cervical vertebra 2, CG4579, School Age Populations, hoja (Spanish, process, processes, red rice <Oryza sativa>, single-organism metabolic process, Solexa sequencing, High-Throughput Sequencing, Calvin Cycle, Gene Expression Profiles, TCV-interacting protein, High Throughput Nucleotide Sequencing, processus, nucleobases, Signature, cellular metabolism, Calvin-Benson, Ion Proton, High-Throughput Nucleotide, Anabolismexact)., Gene Expressions, pattern, second cervical vertebra, distribution, axis, cervical vertebra 2, C2, axis (CII), Gene, C2 vertebra, stalk, axis [C II], Expressions, hoja (Spanish, 葉 (Japanese, culm, axis vertebra, cervical axis, exact), vertebra 2, rice, red rice, Expression, Asian cultivated rice0.00.00.00.00.011412708204811845trueTranscription profiling by high throughput sequencing of rice leaf sectionsIn this study, we examined the transcriptome dynamics within the matured fully expanded rice leaf and used strand-specific RNA sequencing to generate a comprehensive transcriptome dataset for the mature rice leaf. The rice Nipponbare (Oryza sativa l. japonica) seedlings were grown in the greenhouse. About 20 days after planting, the fully opened 4th leaves was cut it into seven 3-cm segments, from bottom to tip and labeled as sections 1 to 7, respectively. The tissues were immediately frozen in liquid nitrogen for total RNA extraction. Two biological replicates were collected for each section. Note: All samples in SRA were assigned the same sample accession (SRS685294). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.2015-08-162016-01-26E-MTAB-43722561979339947