Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

12DAA 20DAA 28DAA RNA-Seq

ABSTRACT: According to the physiological change of the ear leaf, the developing ear leaf after pollination can be divided into three classes: mature leaves [ML, 0–14 days after pollination (DAP)]; early senescent leaves (ESL, 15–24 DAP); and later senescent leaves (LSL, 25–30 DAP). We harvested ear leaves at 12 DAP, 20 DAP, and 28 DAP, representing ML, ESL, and LSL, respectively. To identify genes involved in the leaf senescence process, we sequenced three cDNA libraries, ML (12 DAP), ESL (20 DAP), and LSL (28 DAP) using an Illumina HiSeqTM 2000.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Xiansheng Zhang

PROVIDER: E-MTAB-1709 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptional analyses of natural leaf senescence in maize.

Zhang Wei Yang WY Xu Yong Chao YC Li Wen Lan WL Yang Long L Yue Xun X Zhang Xian Sheng XS Zhao Xiang Yu XY

PloS one 20141222 12

Leaf senescence is an important biological process that contributes to grain yield in crops. To study the molecular mechanisms underlying natural leaf senescence, we harvested three different developmental ear leaves of maize, mature leaves (ML), early senescent leaves (ESL), and later senescent leaves (LSL), and analyzed transcriptional changes using RNA-sequencing. Three sets of data, ESL vs. ML, LSL vs. ML, and LSL vs. ESL, were compared, respectively. In total, 4,552 genes were identified as ...[more]

PMID: 25532107

Similar Datasets

expression data from 14 tissues of maize

Project description:The genes specifically express in some tissue may usually play an important role in the development of the tissue. At vegetative growth stage, some genes may up-regulated to promote the nutrition absorbtion and transportation. However during the reproductive stage, some genes may up-regulated to regulate the flowering and seed development. We used microarrays to identify significantly differentially expressed genes between seed and non-seed tissues. Different tissues of maize were selected at vegetative growth stage and reproductive stage for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify significantly differentially expressed genes between seed and non-seed tissues. To that end, Big trumpet period maize inbred line B73 was use to collect nutritive tissues include root, stem, stem tip and leaf; 10, 15, 20 and 25 DAP (days after pollination) embryo and endosperm; ear and silk before pollination. Each sample has three replications.

2014-01-23 | E-GEOD-54310 | biostudies-arrayexpress

Genotype changes in 8DAP leaf

Project description:Genotype dependent gene expression changes in the leaves of Illinois protein lines at 8 days after pollination (DAP). Illinois protein lines (IPL) comprise lines known as Illinois high protein (IHP), Illinois low protein (ILP), Illinois reverse-low protein (IRLP) and Illinois reverse-high protein (IRHP) lines. These lines represent over a century old experiment containing lines that represent various levels of nitrogen metabolism potential as a function of their grain protein concentration. Microarray experiment was conducted using 8 DAP leaves from the above mentioned four IPLs. Keywords: Genotype response

2009-12-11 | GSE17971 | GEO

Expression analysis of barley glumes vs. endosperm between 0-24 days after pollination

Project description:During grain filling in barley reserves are remobilized from vegetative organs like glumes. In this expression analysis values from glumes and endosperm material were compared from 0 - 24 day after pollination (DAP). This study showed that glumes metabolism and development is adjusted to changing grain demands. Candidate genes are potentially involved in assimilate conversion and translocation.

2015-01-30 | E-MTAB-3040 | biostudies-arrayexpress

Transcription profiling of Capsicum fruit ripening process

Project description:Pepper fruits at four different developmental stages were collected: early fruit [EF; 1 cm long; 7 days after pollination (dap)], mature green fruit (MG; 6-7 cm length; 20 dap), breaking or turning red fruit (BR; fruit are partially red; 35 dap), and red ripe fruit (RR; fully red; 40 dap). Tomato fruits at corresponding developmental stages were also collected: EF (less than 1cm; 7 dap), MG (40 dap), BR (50 dap), and RR (55 dap). For the monitoring of fruit-specific and fruit ripening-related genes, we did array hybridization by using the leaves as a common reference and each corresponding fruit developmental stage sample.

2005-03-01 | E-MEXP-260 | biostudies-arrayexpress

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem

Project description:Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize.

2016-10-15 | GSE81344 | GEO

RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 20 days (D20) shading treatment after pollination, against 20 DAP untreated controls

Project description:Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced two pericarp cDNA libraries, D20 (20 DAP) of shading treatment, and L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000.

2018-03-30 | E-MTAB-6398 | biostudies-arrayexpress

Genome-wide maps of DNA methylation state in rice embryo and endosperm

Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.

2015-09-01 | E-GEOD-57706 | biostudies-arrayexpress

RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 15 days (D15) and 20 days (D20) shading treatment after pollination, against 15 DAP, 20 DAP untreated controls. The purple-grain wheat were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during Octubor, 2015 to June, 2016.

Project description:Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. But little is known about molecular mechanism of anthocyanin biosynthesis. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced four pericarp cDNA libraries, D15 (15 DAP), D20 (20 DAP) of shading treatment, and L15 (15 DAP), L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000. After quality control, raw reads are filtered into clean reads which will be aligned to the reference sequences. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio, and proceed with downstream analysis including gene and isoform expression, deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection. Further, we also perform deep analysis based on different expression genes, including Gene Ontology (GO) enrichment analysis, Pathway enrichment analysis, cluster analysis, and finding transcriptor factor.

2018-03-26 | E-MTAB-5975 | biostudies-arrayexpress

Genotype changes in 8DAP leaf

2010-05-18 | E-GEOD-17971 | biostudies-arrayexpress

Dynamic transcript abundance during cellularisation of the developing barley endosperm: Temporal regulation of cell wall synthesis

Project description:Grain development in the Poaceae defines important end-use properties such as yield, quality and nutritive value. Microarray analyses have been performed on barley grain endosperm extracts from three to eight days after pollination (DAP), when cellularization of the syncytium occurs through the growth of cell walls around individual nuclei. Profiling of transcripts differentially expressed over time reveal 56 specific modules of genes that cluster into 15 groups. Expression patterns have been superimposed upon microscopy data, which identify the timing of key stages in grain development. Thus, cellularization is complete at six DAP, aleurone-related genes can be detected at seven to eight DAP, and starch synthase and hordein genes increase dramatically at seven and eight DAP, respectively. Genes known to be involved in cell wall metabolism are found predominantly in a single module, but analysis using a gene ontology approach splits these genes into four modules, which remain in a single cluster. Transcript levels of the cell wall-related genes peak at seven DAP and the developmental patterns of genes involved in arabinoxylan and (1,3;1,4)-β-glucan synthesis are defined. The transcript data are publicly available (www.etc.) and can be used to interrogate co-expression and differential expression patterns for other groups of genes. In addition, the examination of transcription factor genes that are co-expressed in modules of genes involved in specific processes, such as aleurone differentiation, can be used to identify candidate genes for the control of those particular processes during barley grain development.

2016-02-01 | E-MTAB-2728 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data