Tomato Proteogenomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive Plus
ORGANISM(S): Solanum Lycopersicum (ncbitaxon:4081)
SUBMITTER: 
Justin Walley
PROVIDER: MSV000083363 | MassIVE | Fri Jan 25 09:39:00 GMT 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:affy_hypoctemp_medicago - The characterization of several genotypes of the model Legume Medicago truncatula showed a genetic variability for germination and hypocotyl heterotrophic growth at low temperature and optimal temperature. The most important contrast was between the accessions Jemalong A17 and F83005.5. In order to find genes differently expressed between temperatures and genotypes, the present work focuses on transcriptome profiling during hypocotyl heterotrophic growth under low (10°C) and optimal (20°C) temperature conditions for both genotypes. We used Jemalong A17 and F83005.5 seeds coming from the Medicago truncatula Biological Resource Center in Montpellier, produced in 2006. Experiments were performed in the dark to mimic pre-emergence growth. Pots (6.5 cm diameter, 10 cm high) were incubated in growth chambers either at 10°C or 20°C. They were filled with 500g sand and 100ml of a nutrient solution for young seedlings growth (Saglio and Pradet, 1980). Per pot, five scarified seeds were sown at 1.5 cm depth. Seedlings were harvested at three times: 35°Cd (degree day), 50°Cd and 100°Cd. At each timepoint, about 50 seedlings were harvested and hypocotyl lengths was measured. Hypocotyl were cut and immediately frozen in liquid nitrogen for RNA extractions.
2010-09-10 | GSE18449 | GEO
Project description:Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering. For the study of the genetic-expression pattern over development, 21 seedlings originating from open pollination of olive cultivar M-bM-^@M-^XArbequinaM-bM-^@M-^Y were grown in a greenhouse in Centro IFAPA M-bM-^@M-^\ChurrianaM-bM-^@M-^] MM-CM-!laga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis. Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches. We analyzed samples taken from the seedling/tree No 11, in a dense time-course study by microarray analysis. According to the nature of the samples, i.e. the main apical shoots, we had to use single samples during the first 6 to 15 months of growth. This limits the use of the statistics for this period but is compensated for by providing a series of consecutive data that make it possible to ascertain the time course of gene expression over plant development.
2013-11-09 | E-GEOD-52213 | biostudies-arrayexpress
Project description:affy_hypoctemp_medicago - The characterization of several genotypes of the model Legume Medicago truncatula showed a genetic variability for germination and hypocotyl heterotrophic growth at low temperature and optimal temperature. The most important contrast was between the accessions Jemalong A17 and F83005.5. In order to find genes differently expressed between temperatures and genotypes, the present work focuses on transcriptome profiling during hypocotyl heterotrophic growth under low (10°C) and optimal (20°C) temperature conditions for both genotypes. We used Jemalong A17 and F83005.5 seeds coming from the Medicago truncatula Biological Resource Center in Montpellier, produced in 2006. Experiments were performed in the dark to mimic pre-emergence growth. Pots (6.5 cm diameter, 10 cm high) were incubated in growth chambers either at 10°C or 20°C. They were filled with 500g sand and 100ml of a nutrient solution for young seedlings growth (Saglio and Pradet, 1980). Per pot, five scarified seeds were sown at 1.5 cm depth. Seedlings were harvested at three times: 35°Cd (degree day), 50°Cd and 100°Cd. At each timepoint, about 50 seedlings were harvested and hypocotyl lengths was measured. Hypocotyl were cut and immediately frozen in liquid nitrogen for RNA extractions. Time course of 24 arrays - Medicago
2010-09-10 | E-GEOD-18449 | biostudies-arrayexpress
Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.
2019-10-22 | GSE139160 | GEO
Project description:Sample groupings for this project are as follows: Cauline leaf vs Cultured Cell : - Cauline leaf, p1; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p2; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p3; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cotyledon dark : - Cotyledon, CP1; Exp:Red; Ref: Green (Cy5:Cy3) - Cotyledon, CP2; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cultured cell : - Cotyledon, cn1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon, cn2; Exp:Green; Ref: Red (Cy3:Cy5) Cotyledon dark vs Cultured cell : - Cotyledon dark, n1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n2; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n3; Exp:Green; Ref: Red (Cy3:Cy5) Germinating seed vs Cultured cell : - Germinating seed, gn1; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn2; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl light vs Hypocotyl dark : - Hypocotyl, hldn1; Exp:Red; Ref: Green (Cy5:Cy3) - Hypocotyl, hldn2; Exp:Red; Ref: Green (Cy5:Cy3) Hypocotyl light vs Cultured cell : - Hypocotyl light, hln1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl light, hln2; Exp:Green; Ref: Red (Cy3:Cy5) Petal vs Cultured cell : - Petal, pn1; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn2; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn3; Exp:Green; Ref: Red (Cy3:Cy5) 1DBP vs Cultured cell : - Pistil 1DBP, pin1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin3; Exp:Green; Ref: Red (Cy3:Cy5) Pistil 1DPP vs Cultured cell : - Pistil 1DPP, psn1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn3; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn4; Exp:Green; Ref: Red (Cy3:Cy5) Root dark vs Cultured cell : - Root dark, rdn1; Exp:Green; Ref: Red (Cy3:Cy5) - Root dark, rdn2; Exp:Green; Ref: Red (Cy3:Cy5) Root light vs Cultured cell : - Root light, rln1; Exp:Green; Ref: Red (Cy3:Cy5) - Root light, rlp1; Exp:Red; Ref: Green (Cy5:Cy3) Root light vs Root dark : - Root light vs dark, rldp1; Exp:Red; Ref: Green (Cy5:Cy3) - Root light vs dark, rldp2; Exp:Red; Ref: Green (Cy5:Cy3) Rosette leaf vs Cultured cell : - Rosette leaf, rfp1; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp2; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp3; Exp:Red; Ref: Green (Cy5:Cy3) Sepal vs Cultured cell : - Sepal, sn1; Exp:Green; Ref: Red (Cy3:Cy5) - Sepal, sn2; Exp:Green; Ref: Red (Cy3:Cy5) Silique 3DPP vs Cultured cell : - Silique 3DPP, s3n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n3; Exp:Green; Ref: Red (Cy3:Cy5) Silique 8DPP vs Cultured cell : - Silique 8DPP, s8n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n3; Exp:Green; Ref: Red (Cy3:Cy5) Stamen vs Cultured cell : - Stamen, smn1; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn2; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl dark vs Cultured cell : - Hypocotyl dark, hn1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl dark, hn2; Exp:Green; Ref: Red (Cy3:Cy5) Stem vs Cultured cell : - Stem, stp1; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp2; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp3; Exp:Red; Ref: Green (Cy5:Cy3) Keywords: other
2004-10-24 | GSE1599 | GEO
Project description:Among multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark condition, the rapeseed hypocotyl extended quickly with an apical hook, yellow and folded cotyledon, and the glyoxysome assembling. Whereas under light, the hypocotyl extended slowly, the cotyledon unfolded and turned green. In this study, we performed proteome profiling analyses to show the differential molecular responses of Brassica napus cotyledons to light and dark and reveal metabolic adaptations in postgerminative seedling establishment. In both light and dark-grown conditions.
2017-09-14 | PXD003464 | Pride
Project description:Male C57Bl/6 mice were randomized to undergo 5 days of i) a shiftwork protocol (10-hour light: 10-hour dark cycle) before myocardial infarction (MI) surgery, ii) a normal 12-hour light: 12-hour dark environment before MI surgery, iii) a normal 12-hour light: 12-hour dark environment and used as sham controls, or iv) a shiftwork protocol (10-hour light: 10-hour dark cycle) and used as sham controls. MI surgery was performed on the 5th day, after which all mice were returned to a normal 12-hour light: 12-hour dark cycle. Hearts were collected 24-hours post-MI at ZT06. The microarray approach allows the investigation of transcriptome-wide gene expression changes in hearts from mice on a shiftwork cycle or on a regular light:dark cycle before MI.
2018-11-30 | GSE123092 | GEO
Project description:Transcriptional profiling of hypocotyl comparing wild type with shr mutant. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SHORT-ROOT on growth and development of Arabidopsis shoot system (hypocotyl) by global transcriptome analysis and to identify the key players in the regulatory pathway.
2021-12-28 | GSE97670 | GEO
Project description:The Oryza longistaminata is a perennial wild rice species with AA genome, which characterized by the presence of rhizomatous stem. The rhizomatousness trait in rice was previously identified quantitatively controlled by many genes, but the molecular mechanism related to the rhizome initiation and elongation is still unknown. In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform, the rhizome-specific expressed genes and its corresponding regulatory were further analyzed. The different gene sets were determined exclusively expressed in five tissues; strikingly 58 genes with functions related to transcription regulation and cell proliferation were identified as prevalent sets in rhizome tip, of them, several genes were functionally involved in tiller initiation and elongation. And a set of genes were differentially regulated in the rhizome tip relative to shoot tip, the predominant repressed genes are involved in photosynthesis, while genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in rhizome tip or internode, and two cis-elements such as RY repeat and TAAAG, which implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the rhizome related gene cloning. The whole genome profiling of oryza longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and there might be an overlapping regulatory mechanism in the establishment of rhizome and tiller. Phytohormone such as IAA and GA are involved in the signaling pathway in determining rhizome. Several cis-elements enriched in rhizome and the identified rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism of rhizomatousness In this study, the specific gene expression patterns across five tissues including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform.
2010-10-31 | E-GEOD-24228 | biostudies-arrayexpress
Project description:The transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis) is one of the most critical in plant development. Here the newly identified mutant dez is photomorphogenic in the dark and is strongly enhanced in high Zn. dez displays a shortened hypocotyl, expanded cotyledons, an elongated root and differentiated plastids in the dark contrast to wild-type seedlings that are typically skotomorphogenic, with a long hypocotyl and unexpanded cotyledons protected by an apical hook, and undifferentiated etioplasts We used microarrays to identify transcripts regulated in dez in high-Zn relative to wild-type in high-Zn, and dez in high-Zn relative to dez in control conditions.
2017-11-02 | GSE96589 | GEO