Expression analysis of maize (Zea mays L.) genes in continuous light
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays Zea mays subsp. mays
PROVIDER: GSE55524 | GEO | 2014/03/04
SECONDARY ACCESSION(S): PRJNA239875
REPOSITORIES: GEO
Similar Datasets
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. A nine chip (Biogemma Nimblegen Custom Array) study using total RNA recovered from three replicates (plants) sampled every 12 hours (1h before and 12 and 24h after lights on).
2014-03-04 | E-GEOD-55524 | 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
Project description:Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library.
2010-12-10 | GSE25994 | GEO
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: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:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have over 37,000 informative spots from maize. Statistical analyses showed that approximately 7.4% and 6.0% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. Keywords: cell type comparison design
2007-06-07 | GSE6267 | GEO
Project description:Transcriptome of Zea mays genotypes under control and stress conditions. Stress conditions include heat, cold, salt, and UV. We extracted and sequenced RNA from 14 day old seedlings of inbred lines B73, Mo17 and Oh43 grown using standard conditions as well as seedlings that had been subjected to cold (5°C for 16 hours), heat (50°C for 4 hours), high salt (watered with 300 mM NaCl 20 hours prior to collection) or UV stress (2 hours). For each stress the plants were sampled immediately following the stress treatment and there were no apparent morphological changes in these plants relative to control plants.
2015-01-31 | E-MTAB-4258 | biostudies-arrayexpress
Project description:Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.
2010-12-10 | E-GEOD-25994 | biostudies-arrayexpress
Project description:Sequencing of the maize B73 transcriptome
2012-06-21 | E-MTAB-4296 | biostudies-arrayexpress
Project description:Genome-wide mapping of the TSS in root and shoot from two maize lines B73 and A632 Genome-wide locations and dynamics of maize core promoters obtained from the experimental establishment of the TSSs coordinates. The work derived from this data it is the first genome-wide atlas of core promoters and its dynamic generated for an important crop species.
2015-11-04 | GSE70251 | GEO