Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244949 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation profiling in epiRIL344 BC1-S1 to BC1-S6 aerial part (epiRIL344_BC1-S1 - epiRIL344_BC1-S2 - epiRIL344_BC1-S3 - epiRIL344_BC1-S4 - epiRIL344_BC1-S5 - epiRIL344_BC1-S6) Keywords: Genome binding/occupancy profiling by genome tiling array
2012-09-03 | GSE37285 | GEO
Project description:DNA methylation profiling in epiRIL344 BC1-S1 to BC1-S6 aerial part (epiRIL344_BC1-S1 - epiRIL344_BC1-S2 - epiRIL344_BC1-S3 - epiRIL344_BC1-S4 - epiRIL344_BC1-S5 - epiRIL344_BC1-S6) Keywords: Genome binding/occupancy profiling by genome tiling array 1 biological replicate in dye-swap - MeDIP-chip
2012-09-03 | E-GEOD-37285 | biostudies-arrayexpress
Project description:The timing of flower opening is essential for pollination and thus seed production. Despite flower opening has been a long lasting topic for plant biologists, the underling molecular mechansim remains elusive. Here we used a unique cucumber line â6457â that spontaneously produces super ovary with delayed corolla opening as material, and explored the physiological, cytological, nutritional and transcriptomic reasons for the delayed corolla opening in super ovary. Our data showed that cell division and cell expansion persisited for a longer period of time in the super ovary, especially during the green yellow bud stage and yellow bud stage. Similarly, RNA-seq analyses showed that RNA and protein synthesis related genes were upregulated during these two stages, which may account for the decreased nitrogen and phosphrate content in the super ovary. Further, activation of transcription factors were delayed in the green yellow bud stage, while signalling kinases related genes were upregulated in the yellow bud stage in the super ovary. Photosynthesis related genes were also significantly activated in the super ovary, which corresponds to the increased soluble suble content. Phytohoromones such as cytokinins and gibberllins were elevated in the super ovary. Consistently, cytokinins and gibberllins related genes showed significantly enhanced expression. Therefore, both developmental and nutritional factors regulate the timing of female flower opening in cucumber, and provide a valuable foundation for dissecting the underling regulatory pathways of flower opening in planta. The normal ovary blooms at 4-5 days after labeling (when the ovary is visible) (DAL), with the majority blooms at 5 DAL, while the anthesis of super ovary occurs at 8-9 DALs, with most super ovaries blooms at 9 DAL.In the normal ovary, corolla at 1 DAL (N1), 3 DAL (N3), 4 DAL (N4), and 5 DAL (N5) is the typical stage for green bud, green yellow bud, yellow bud, and flowering, respectively, whereas in the super ovary, corolla at 1 DAL (S1) is the green bud, corolla at 3, 4 and 5 DAL (S3, S4, S5) is the green yellow bud, corolla at 7 and 8 DAL (S7, S8) is the yellow bud, and corolla at 9 DAL (S9) is the typical flowering stage.Transcriptome profiling of 11 stages include N1,N3,N4,N5,S1,S3,S4,S5,S7,S8 and S9 were performed, and each stage had 3 biological replicates.
2016-07-25 | E-GEOD-76358 | biostudies-arrayexpress
Project description:Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied.
2008-07-08 | GSE12006 | GEO
Project description:Olive (Olea europaea L.) is one of the most economically relevant tree crops in the Mediterranean basin. In this study, a comparative proteomic along with metabolomic-wide investigation was carried out on drupes of Greek olive cultivar 'Chondrolia Chalkidikis', collected across six developmental stages (S), namely seed development (S1, S2), mesocarp development (S3, S4, S5) and full maturation (S6). These stages were first characterized through the dynamics of fruit weight, dimensions and color parameters such as lightness, redness and yellowness. Combined gas chromatography–mass spectrometry and reversed–phase liquid chromatography quadrupole–time–of–flight mass spectrometry (RPLC–QToF–MS) procedures quantified 47 primary (e.g. allose, galactose, quinic acid, sorbitol, stearic acid) and 21 secondary (e.g. elenolic acid, oleacin, rutin, luteolin, hydroxytyrosol) metabolites in mesocarp samples during development. Protein analysis via nano–LC coupled to HDAM Orbitrap mass spectrometer, identified 3258 proteins from which the 350 were differentially accumulated between the final maturation stages (S5 and S6). Olive genome-based functional annotation showed that the largest proportion of identified proteins were involved in primary metabolism [i.e. lipoxygenases (LOX1/5)], energy [i.e. ferredoxin NADP+ reductase (FNR)], signal transduction [i.e. serine/threonine kinases (SAPK2, SRK2A, STK), transcription [i.e. elongation factor 2 (EEF2)] and protein destination [i.e. serine carboxypeptidase (SCPL)]. This investigation provides a reference framework for further nutritional and breeding studies, also allowing cross comparison among other olive cultivars.
2021-11-25 | PXD021086 | Pride
Project description:We analysed transcriptome changes between seed devlopement (4 stages corresponding at before (S1) and after (S2) desiccation tolerance acquisition and before (S3) and after (S4) longevity acquisition) in dissected seed tissues (embryo, E; Endosperm Eo and Seed Coat SC)
2020-11-03 | GSE160725 | GEO
Project description:Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied. Experiment Overall Design: Four microarray chips were analyzed: Experiment Overall Design: S1 was taken 15 min before the oxygen downshift Experiment Overall Design: S2, S3 and S4 were taken 15 min, 45 min and 75 min after the oxygen downshift, respectively
2008-10-21 | E-GEOD-12006 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of parental, ABT-199 resistant population, and ABT-199 resistant clones from 3 acute myelogenous leukemia (AML) cell lines (MOLM-13, MV-4-11, OCI-AMLO2). The Illumina Infinium MethylationEPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs from AML cell line samples. Samples include 4 ABT-199 sensitive parental MOLM-13 population samples, 4 ABT-199 resistant MOLM-13 population samples, 3 ABT-199 resistant MOLM-13 S2 clone samples, 3 ABT-199 resistant MOLM-13 S5 clone samples, 4 ABT-199 resistant MOLM-13 S6 clone samples, 3 ABT-199 sensitive parental MV-4-11 population samples, 3 ABT-199 resistant MV-4-11 population samples, 3 ABT-199 sensitive parental OCI-AML2 population samples, 3 ABT-199 resistant OCI-AML2 population samples, 3 ABT-199 resistant OCI-AML2 S1 clone samples, 3 ABT-199 resistant OCI-AML2 S2 clone samples, 3 ABT-199 resistant OCI-AML2 S8 clone samples.
2022-01-12 | GSE193254 | GEO
Project description:To provide further insight to the signaling pathways deregulated by SPOP mutation and determine the relevance of these models to human prostate cancer, we performed RNA-seq on SPOP mutant organoids and controls. RNA-seq reads mapped to human and mouse SPOP confirmed appropriate expression of the F133V transgenic transcript without overexpression compared to endogenous mouse Spop. Quantification of gene expression was performed via RSEQtools using GENCODE as reference gene–annotation set. Both SPOPmut and SPOPwt were done in the same run. S0 was done in first run; S1 and S2 were done in second run. S3, S4 and S5 were done in third run. S5mut and S5wt were excluded from differentially expressed genes analysis, due to the different mouse line.
2017-03-13 | GSE94839 | GEO
Project description:The study investigated protein dynamics throughout fruit developmental and ripening process of blue-colored bilberry. The proteomic approach was applied to study at four different ripening stages, S2-small green fruit, S3- large green fruit, S4- purple ripening fruit, S5- ripe, blue fruit of bilberry. Regulatory network of plant hormones and physiological processes occurring during bilberry fruit ripening was revealed for the first time. The white-colored mutant bilberry, at the ripe stage, was also investigated differences compared to wild, blue-colored berries.
2024-09-18 | PXD047290 | Pride