Project description:Chlorophyll plays critical roles in photosynthetic light harvesting, energy transduction and plant development. In this study, a novel wucai (Brassica campestris L.) germplasm with green outer leaves and yellow inner leaves at the adult stage (W7-2) was used to examine chlorophyll metabolism response to cold acclimation. A green leaf wucai genotype without leaf color changes named W7-1 was selected as the control to evaluate the chlorophyll metabolism changes of W7-2. Compared to W7-1, the contents of chlorophyll a (Chl a) and chlorophyll b (Chl b) in W7-2 were significantly reduced at five developmental stages (13, 21, 29, 37 and 45 days after planting (DAP). An iTRAQ-based quantitative proteomic analysis was carried out at 21 and 29 DAP according to the leaf color changes in both of genotypes. A total of 1409 proteins were identified, of which 218 showed differential accumulations between W7-2 and W7-1 during the two developmental stages.
Project description:This dataset contains 48 RNA-seq samples from Triticum aestivum cv. Paragon plants grown under field conditions as part of the WGIN 2016 diversity trial. Flag leaf node tissues were harvested at eight time points following anthesis to capture transcriptional changes associated with senescence progression. Plants were subjected to two nitrogen fertilisation treatments (100 and 200 kg N ha⁻¹), with three biological replicates per treatment and time point. The selected time points for each nitrogen level were: N100 – 0, 7, 14, 21, 25, 28, 31, and 34 days post-anthesis (DPA); N200 – 0, 7, 14, 21, 28, 32, 35, and 38 DPA. This time-course RNA-seq dataset enables the investigation of gene expression dynamics during post-anthesis senescence in wheat flag leaf nodes, which serve as central hubs for nutrient trafficking during grain filling.
Project description:blanc-08-01_2012_01_rnapaths_03 - rnapaths--3_02/2012 - Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT. - Identify transcripts that are significantly changed in double mutants (L1 vcs sgs2) (xrn4-5/sgs3-11) versus their respective single mutants (L1 vcs and L1 sgs2) (xrn4-5 and sgs3-11) , and identify transcripts that are changed among the single and double mutants compared to WT (Col) reference or to mutant L1 reference. 20 dye-swap - genotype comparaison
Project description:Interleukin-21 (IL-21) is a pleiotropic cytokine that induces expression of transcription factor BLIMP1 (encoded by Prdm1), which regulates plasma cell differentiation and T cell homeostasis. We identified an IL-21 response element downstream of Prdm1 that binds the transcription factors STAT3 and IRF4, which are required for optimal Prdm1 expression. Genome-wide ChIP-Seq mapping of STAT3- and IRF4-binding sites showed that most regions with IL-21-induced STAT3 binding also bound IRF4 in vivo, and furthermore, revealed that the noncanonical TTCnnnTAA GAS motif critical in Prdm1 was broadly used for STAT3 binding. Comparing genome-wide expression array data to binding sites revealed that most IL-21-regulated genes were associated with combined STAT3-IRF4 sites rather than pure STAT3 sites. Correspondingly, ChIP-Seq analysis of Irf4_/_ T cells showed greatly diminished STAT3 binding after IL-21 treatment, and Irf4_/_ mice showed impaired IL- 21-induced Tfh cell differentiation in vivo. These results reveal broad cooperative gene regulation by STAT3 and IRF4. Affymetrix expression data: Prepare CD4+ T cells from spleen. CD4+ T cells were preactivated, rested, and treated with IL-21 for 1, 6, and 24 hours. ChIP-seq data: Profiling of IRF4 and Stat3 binding with and without IL-21 stimulation in wild type and IRF4 KO mice.
Project description:This project constructed a multiomics (proteome, metabolome, and transcriptome) database on the response of purslane (Portulaca oleracea L.) plants to salt stress and subsequently started to employ Single-omics (SOA) and Multi-omics Integration (MOI) strategies to characterize the molecular basis of the resistance to salinity stress found in this halophyte species. After evaluating the morpho-physiological responses of purslane plants to salinity stress using a robust salinity stress protocol developed in-house, leaves, and roots were used to generate the database. The proteome data from five plants (control and salt-stressed - leaf and root) was generated and then submitted to the MaxQuant software version 2.1.3.0 for protein identification and abundance, generating a .txt file named “proteinsgroups” that underwent statistical analysis in Perseus software version 2.0.5.0. Here the data and results of the proteome part of the project are presented. For additional information, please read: Silva, V. N. B., da Silva, T. L. C., Ferreira, T. M. M., Neto, J. C. R., Leão, A. P., de Aquino Ribeiro, J. A., Abdelnur, P. V., Valadares, L. F., de Sousa, C. A. F., & Júnior, M. T. S. (2022). Multi-omics Analysis of Young Portulaca oleracea L. Plants' Responses to High NaCl Doses Reveals Insights into Pathways and Genes Responsive to Salinity Stress in this Halophyte Species. Phenomics (Cham, Switzerland), 3(1), 1–21. https://doi.org/10.1007/s43657-022-00061-2
Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series