Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories (ATAC-seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA694064 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR13506473_1.fastq.gz | Fastqsanger.gz | |||
| SRR13506473_2.fastq.gz | Fastqsanger.gz | |||
| SRR13506475_1.fastq.gz | Fastqsanger.gz | |||
| SRR13506475_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 37 |
Similar Datasets
Project description:Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories (scRNA-seq)
| PRJNA694066 | ENA
Project description:Immune and tissue stem cells retain an epigenetic memory of inflammation that intensifies sensitivity to future encounters. Here, we address whether and to what consequence stem cells possess and accumulate memories of diverse experiences. Monitoring a choreographed response to wounds, we find that as hair follicle stem cells leave their niche, migrate to repair damaged epidermis and take up long-term foreign residence there, they accumulate long-lasting epigenetic memories of each experience, culminating in post-repair epigenetic adaptations that sustain the epidermal transcriptional program and surface barrier. Each memory has its own physiological impact, collectively endowing these stem cells with heightened regenerative ability to heal wounds and broadening their tissue regenerating tasks compared to their naïve counterparts. These findings have profound implications for tissue fitness and aging.
2021-11-29 | GSE165314 | GEO
Project description:Immune and tissue stem cells retain an epigenetic memory of inflammation that intensifies sensitivity to future encounters. Here, we address whether and to what consequence stem cells possess and accumulate memories of diverse experiences. Monitoring a choreographed response to wounds, we find that as hair follicle stem cells leave their niche, migrate to repair damaged epidermis and take up long-term foreign residence there, they accumulate long-lasting epigenetic memories of each experience, culminating in post-repair epigenetic adaptations that sustain the epidermal transcriptional program and surface barrier. Each memory has its own physiological impact, collectively endowing these stem cells with heightened regenerative ability to heal wounds and broadening their tissue regenerating tasks compared to their naïve counterparts. These findings have profound implications for tissue fitness and aging.
2021-11-29 | GSE165312 | GEO
Project description:Immune and tissue stem cells retain an epigenetic memory of inflammation that intensifies sensitivity to future encounters. We investigated whether and to what consequence stem cells possess and accumulate memories of diverse experiences. Monitoring a choreographed response to wounds, we found that as hair follicle stem cells leave their niche, migrate to repair damaged epidermis, and take up long-term foreign residence there, they accumulate long-lasting epigenetic memories of each experience, culminating in post-repair epigenetic adaptations that sustain the epidermal transcriptional program and surface barrier. Each memory is distinct, separable, and has its own physiological impact, collectively endowing these stem cells with heightened regenerative ability to heal wounds and broadening their tissue-regenerating tasks relative to their naïve counterparts.
| S-EPMC8896201 | biostudies-literature
Project description:Remembrances of traumata range among the most enduring forms of memories. Despite the elevated lifetime prevalence of anxiety disorders, effective strategies to attenuate long-term traumatic memories are scarce. The most efficacious treatments to diminish recent (i.e., day-old) traumata capitalize on memory updating mechanisms during reconsolidation that are initiated upon memory recall. Here, we show that in mice successful reconsolidation-updating paradigms for recent memories fail to attenuate remote (i.e., month-old) ones. We find that whereas recent memory recall induces a limited period of hippocampal neuroplasticity mediated, in part, by S-nitrosylation of HDAC2 and histone acetylation, such plasticity is absent for remote memories. However, by using an HDAC2-targeting inhibitor (HDACi) during reconsolidation, even remote memories can be persistently attenuated. This intervention epigenetically primes the expression of neuroplasticity-related genes as revealed by whole genome RNA sequencing, which is accompanied by higher metabolic, synaptic and structural plasticity. Thus, applying HDACis during memory reconsolidation might constitute a treatment option for remote traumata. 3 biological replicates per group were analyzed. The material analyzed was whole hippocampi from one brain hemisphere, from which total RNA was extracted.
2014-01-04 | E-GEOD-53794 | biostudies-arrayexpress
Project description:Remembrances of traumata range among the most enduring forms of memories. Despite the elevated lifetime prevalence of anxiety disorders, effective strategies to attenuate long-term traumatic memories are scarce. The most efficacious treatments to diminish recent (i.e., day-old) traumata capitalize on memory updating mechanisms during reconsolidation that are initiated upon memory recall. Here, we show that in mice successful reconsolidation-updating paradigms for recent memories fail to attenuate remote (i.e., month-old) ones. We find that whereas recent memory recall induces a limited period of hippocampal neuroplasticity mediated, in part, by S-nitrosylation of HDAC2 and histone acetylation, such plasticity is absent for remote memories. However, by using an HDAC2-targeting inhibitor (HDACi) during reconsolidation, even remote memories can be persistently attenuated. This intervention epigenetically primes the expression of neuroplasticity-related genes as revealed by whole genome RNA sequencing, which is accompanied by higher metabolic, synaptic and structural plasticity. Thus, applying HDACis during memory reconsolidation might constitute a treatment option for remote traumata.
2014-01-04 | GSE53794 | GEO
Project description:Mixed species in three open PHA accumulating bioreaactors Raw sequence reads
| PRJNA360897 | ENA
Project description:Microglia protect memories formed during sleep deprivation
| PRJNA728892 | ENA
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root Genes expression was compared between cotton stems that were low in starch and accumulating starch. Gene expression was also compared between cotton roots that were low in starch and accumulating starch. A total of three microarrays were used. One dye swap was used. Material from the field were harvested 2 weeks apart. Greenhouse grown material were planted at two week intervals and harvested at the same time. NOTE that the channel representing the low starch material only gave about half of the total signal than the high starch samples. QPCR of 9 genes confirmed differential expression of 8 of them. QPCR also confirmed similar expression of two genes not predicted to be differentially expressed by the microarray analysis. Therefore no correction was made for the apparent difference in the hybridization of high and low starch samples.
2010-06-24 | E-GEOD-8973 | biostudies-arrayexpress
Project description:Transcriptional profiling of mouse induced pluripotent stem (iPS) cells with the low potency (strain 20D17) compared to control iPS cells with the normal potency (strain 38C2). Two-condition experiment: iPS cells strain 20D17 vs. control iPS cells strain 38C2. Biological replicates: 2 strain 20D17, 2 strain 38C2, independently grown and harvested. One replicate per array.
2010-06-23 | E-GEOD-18117 | biostudies-arrayexpress