This SuperSeries is composed of the SubSeries listed below.
Cell identity regulators link development and stress responses in the Arabidopsis root.
Age, Specimen part, Treatment
View SamplesCell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under standard pH (pH 5.7) or roots that had been transfered to low pH (pH 4.6) media for 24 hours.
Cell identity regulators link development and stress responses in the Arabidopsis root.
Specimen part
View SamplesTo understand the effect of low pH on developmental stages in the root, we dissected the root into four developmental zones after exposure to low pH and expression profiled each zone.
Cell identity regulators link development and stress responses in the Arabidopsis root.
Age
View SamplesCell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under sulfur deficient conditions for 3 hours.
Cell identity regulators link development and stress responses in the Arabidopsis root.
Specimen part
View SamplesWe preformed at time-course of the expression of whole Arabidopsis roots for 3H, 12H, 24H, 48H and 72H after transfer to media lacking sulfur. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots.
Cell identity regulators link development and stress responses in the Arabidopsis root.
No sample metadata fields
View SamplesTo understand the effect of sulfur deficiency on developmental stages in the root, we dissected the root into four developmental zones after exposure to sulfur deficiency and expression profiled each zone.
Cell identity regulators link development and stress responses in the Arabidopsis root.
No sample metadata fields
View SamplesTo estimate the effect of protoplasting and sorting on low pH-regulated gene expression, we generated expression profiles for whole roots treated with low pH for 24 hours and whole roots that had been protoplasted and FACS sorted after 24 hours of exposure to low pH.
Cell identity regulators link development and stress responses in the Arabidopsis root.
Treatment
View SamplesNotch1 signaling is absolutely essential for steady-state thymic lymphopoiesis, but the role of other Notch receptors, and their potential overlap with the function of Notch1, remains unclear. Here we show that like Notch1, Notch3 is differentially expressed by progenitor thymocytes, peaking at the DN3 progenitor stage. Using mice carrying a gene-trapped allele, we show that thymic cellularity is slightly reduced in the absence of Notch3, although progression through the defined sequence of TCR- development is normal, as are NKT and TCR cell production.
Nonoverlapping functions for Notch1 and Notch3 during murine steady-state thymic lymphopoiesis.
Sex, Age, Specimen part
View SamplesExercise attenuates the development of chronic non-communicable diseases (NCDs). Gene signaling pathway analysis offers an opportunity to discover if electrically induced muscle exercise regulates key pathways among people living with spinal cord injury (SCI). We examined short-term and long-term durations of electrically induced skeletal muscle exercise on complex gene signaling pathways, specific gene regulation, and epigenetic tagging of PGC1a, a major transcription factor in skeletal muscle of men with SCI. After short or long-term electrically induced exercise training, participants underwent biopsies of the trained and untrained muscles. RNA was hybridized to an exon microarray and analyzed using a gene set enrichment analysis. We discovered that long-term exercise training regulated the Reactome gene sets for Metabolism (38 gene sets), Cell Cycle (36 gene sets), Disease (27 gene sets), Gene Expression and Transcription (22 gene sets), Organelle Biogenesis (4 gene sets), Cellular Response to Stimuli (8 gene sets), Immune System (8 gene sets), Vesicle Mediated Transport (4 gene sets), and Transport of Small Molecules (3 gene sets). Specific gene expression included: Oxidative catabolism of glucose including PDHB (p<0.001), PDHX (p<0.001), MPC1 (p<0.009), and MPC2 (p<0.007); Oxidative phosphorylation genes including SDHA (p<0.006), SDHB (p<0.001), NDUFB1 (p<0.002), NDUFA2 (p<0.001); Transcription Genes including PGC1α (p<0.030) and PRKAB2 (p<0.011); Hypertrophy gene MSTN (p<0.001); and the Myokine generating FNDC5 gene (p<0.008). Long-term electrically induced exercise de-methylated the major transcription factor, PGC1a. Taken together, these findings support that long term electrically induced muscle activity regulates key pathways associated with muscle health and systemic metabolism.
Impact of short- and long-term electrically induced muscle exercise on gene signaling pathways, gene expression, and PGC1a methylation in men with spinal cord injury.
Sex, Specimen part, Disease
View SamplesWe sorted for GFP+ cells using the enhancer trap J0571 with the UAS promoter driving the expression of different BIRD genes. Different genetic backgrounds are use and listed below.
Transcriptional control of tissue formation throughout root development.
Specimen part
View Samples