Zea mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1057593 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand how the NAC transcription factor KIL1 regulates age-induced senescence and cell death in maize silks, we need to get a genome-wide view on its downstream targets. We propose to compare the transcriptome profiles of GOF and LOF transgenic silk tissue with the profile of wild-type B104 silk. 1 cm of basal part of silk from rings 6-10 from plants harboring the dominant-negative repressor proSILK1:KIL1-SRDX, proSILK1:KIL1 overexpressing line, and wild type B104 will be harvested at 11 DASE. This will allow to compare and contrast the expression profiles of KIL1 LOF and GOF mutants with transcriptome data derived from wild type senescent silk.
2022-08-16 | E-MTAB-10850 | biostudies-arrayexpress
Project description:The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. We compared the transcriptome profile of the third node in la1-ref mutants with those in wild-type plants using RNA-SEQ to examine the genome-wide effect of the ZmLA1 gene. We generated 14.6 and 36.5 million paired-end reads from two biological samples of wild-type and la1-ref mutant plants, respectively.
2013-11-20 | E-MTAB-4196 | biostudies-arrayexpress
Project description:Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. For maize RNA-seq analysis, pooled tissues from three, eight-day-old maize seedlings were collected from transgenic and wild-type plants, prior to or after 2-hour dehydration, to conduct the RNA-seq analysis.
2015-03-29 | E-MTAB-4246 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2009-12-31 | GSE17339 | GEO
Project description:Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome.
2015-02-04 | GSE54166 | GEO
Project description:Investigation of whole genome gene expression level changes in maize plants (standard maize line B73) in controlled conditions under continuous light. Tissues of the leaf elongation zone were sampled from plants well watered every 12 hours before and after lights on.
2014-03-04 | GSE55524 | GEO
Project description:Sequencing of the maize B73 transcriptome
2012-06-21 | E-MTAB-4296 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.
2009-12-31 | E-GEOD-17339 | biostudies-arrayexpress
Project description:Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues.
2014-08-09 | E-MTAB-4395 | biostudies-arrayexpress
Project description:These data include RNA-seq, circRNA-seq, and small RNA-seq of transcriptome, Ribo-seq of translatome and protein protein binary interactions by recombination-based library vs. library yeast-2-hybrid throughout the lifecycle of the maize inbred line B73.
2022-12-25 | GSE160288 | GEO