Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA349462 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4435490_1.fastq.gz | Fastqsanger.gz | |||
| SRR4435490_2.fastq.gz | Fastqsanger.gz | |||
| SRR4435500_1.fastq.gz | Fastqsanger.gz | |||
| SRR4435500_2.fastq.gz | Fastqsanger.gz | |||
| SRR4435510_1.fastq.gz | Fastqsanger.gz |
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Project description:Genome-wide changes in chromatin accessibility in CD8 T cells during viral infection
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Project description:The goal of this study was to identify the molecular programming using ATAC-seq of CD8 T cells responding to different viral infections. Mice were infected with either LCMV Armstrong to model an acute infection or LCMV Clone-13 to model a chronic infection. At various time points following infection, virus-specific CD8 T cells were purified and ATAC-seq performed. These data identify the changes in chromatin accessibility associated with acute infections and the establishment of functional memory versus those accessibility changes associated with chronic infection.
2017-01-31 | GSE83081 | GEO
Project description:Changes in chromatin accessibility assocaiated with CD8 T cell responses to viral infections
| PRJNA325011 | ENA
Project description:In response to acute infection, naive CD8+ T cells expand, differentiate into effector cells and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8+ T cells acquire an “exhausted” phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8+ T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq. Acquisition of effector, memory or exhausted phenotypes was associated with stable changes in chromatin accessibility away from the naive T cell state. Regions differentially accessible between functional subsets in vivo were enriched for binding sites of transcription factors known to regulate these subsets, including E2A, BATF, IRF4, T-bet and TCF1. Exhaustion-specific accessible regions were enriched for consensus binding sites for NFAT and Nr4a family members, indicating that chronic stimulation confers a unique accessibility profile on exhausted cells.
2016-12-13 | GSE88987 | GEO
Project description:Compendium of high-throughput sequencing datasets derived from murine CD8+ T cells responding to infection, profiled by RNA-seq, ChIP-seq, and ATAC-seq at Naïve, Effector, and Memory timepoints across the Kaech, Goldrath, and Pereira labs, and ChIP-seq of various transcription factors across several labs Submission contains both original data from the Kaech lab and reanalysis of data from the Pereira and Goldrath labs, as well as various other labs corresponding to individual transcription factor ChIP-seq datasets, totaling to 96 reanalyzed GSM samples across several GSE series Included GSE series are: GSE95237 (Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets), GSE95238 (Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation), GSE88987 (Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection), GSE58075 (Genome-wide mapping of Myc, AP4, and phosphorylated RNA polymerase II binding in activated CD8 T cells by ChIP sequencing), GSE54191 (ChIP-Seq analysis of BATF, IRF4, the Jun proteins, and histone modifications in effector CD8+ T cells), GSE20898 (Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types), GSE46943 (Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [ChIP-Seq]), GSE72997 (ChIP-Seq analysis of Helios and histone modifications in CD4+ and CD8+ Tregs), GSE50128 (Genome-wide maps of Runx3 bound regions in splenic IL-2-activated CD8+ T cells), GSE72565 (Binding of STAT5 upon IL-2 treatment to genomic sites in mouse CD8 T cells costimulated in vivo through CD134 plus CD137), GSE49930 (The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells [ChIP-seq]), and GSE52070 (Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells)
2018-03-17 | GSE111902 | GEO
Project description:Chronic viral infection disrupts memory B cell development. We used single cell ATAC sequencing (scATAC-seq) to analyze chromatin accessibility in antigen-specific B cells responding to acute versus chronic LCMV infection.
2024-02-17 | GSE225932 | GEO
Project description:To gain insights into how PBAF complex regulates dynamic chromatin structure changes in LCMV-specific CD8+ T cells during chronic viral infection and examine the how PBAF-deficiency alters the transcriptional and epigenetic heterogeneity of CD8+ T cells, we performed single cell RNA + ATAC multiomic sequencing on Arid2- and Pbrm1-deficient CD8+ T cells and their wild-type counterpart.
2023-06-22 | GSE222346 | GEO
Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
| S-EPMC8784167 | biostudies-literature
Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
2004-01-02 | GSE887 | GEO
Project description:To further understand the chromatin accessibility changes between early and late CD8 T cell populations responding to acute and chronic infections we performed ATAC-seq on early Stem-like, effector and late Stem-like and effector populations.
2025-01-11 | GSE269785 | GEO