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Items: 1 to 20 of 21058

1.

Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain

(Submitter supplied) Retroviruses cause lifelong infections resulting from their ability to thwart innate immunity. The Apobec family of cytidine deaminases are part of the innate immune response that recognizes and mutates foreign nucleic acids, including those from multiple viruses. Multiple retroviral antagonists of Apobecs have been identified, including mouse mammary tumor virus (MMTV)-encoded Rem protein. Previous experiments have shown that Rem-null MMTV or closely related TBLV proviruses from BALB/c tumors accumulate G-to-A and C-to-T mutations typical of Apobecs compared to wild-type proviruses expressing Rem. more...
Organism:
Mus musculus
Type:
Other
Platforms:
GPL16417 GPL24973
30 Samples
Download data: CSV
Series
Accession:
GSE263741
ID:
200263741
2.

Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation

(Submitter supplied) we compare the TCR repertoires of MAIT1 and MAIT17 cells from the mouse thymus using 5’ scRNAseq and scTCRseq of MR1:5-OP-RU tetramer positive thymocytes. A thorough analysis of TCR features between MAIT sub-populations did not show any difference between the repertoires of MAIT1 and MAIT17 subsets. Quantitative simulation of clonotype distributions of MAIT1 and MAIT17 cells allowed us to investigate the role of TCR characteristics in MAIT fate choice, and to pinpoint the stage at which lineage commitment occurs. more...
Organism:
Mus musculus
Type:
Other
Platforms:
GPL24247 GPL16417
3 Samples
Download data: CSV, MTX, TSV, TXT
Series
Accession:
GSE236666
ID:
200236666
3.

Base editing of Ptbp1 in neurons alleviates symptoms in a Parkinson’s disease mouse model

(Submitter supplied) Parkinson’s disease (PD) is a multifactorial disease caused by irreversible progressive loss of dopaminergic neurons. Recent studies reported successful conversion of astrocytes into dopaminergic neurons by repressing polypyrimidine tract binding protein 1 (PTBP1), which led to a rescue of motor symptoms in a mouse model for PD. However, the mechanisms underlying this cell type conversion remain underexplored and controversial. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
80 Samples
Download data: TXT
Series
Accession:
GSE237570
ID:
200237570
4.

Development of a ß-Globin Gene Replacement Strategy as a Therapeutic Approach for ß-Hemoglobinopathies

(Submitter supplied) β-hemoglobinopathies are the most common genetic disorders worldwide. In sickle cell disease (SCD) a single mutation (E6V) in the b-globin (HBB) gene results in dysfunctional hemoglobin protein, while in β-thalassemia, over 300 mutations distributed across the HBB gene are known to reduce the production of β-globin and cause severe anemia. A genetic engineering approach that replaces the whole HBB gene is an ideal strategy to rescue HBB expression for most genotypes but is technically challenging as the insert cannot be homologous to the endogenous gene and codon-optimized, intron-less sequences may not reconstitute adequate HBB levels. more...
Organism:
Mus musculus; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Other
Platforms:
GPL24676 GPL28352 GPL16417
69 Samples
Download data: CSV, TXT, VCF
Series
Accession:
GSE229212
ID:
200229212
5.

Intragraft memory-like CD127hiCD4+Foxp3+ regulatory T cells maintain transplant tolerance

(Submitter supplied) CD4+Foxp3+ regulatory T cells (Tregs) play an essential role in suppressing transplant rejection but their role within the graft, is poorly understood. To address this, we compared phenotypic and transcriptomic characteristics of Treg populations within lymphoid-organs and grafts in an islet xenotransplant model of tolerance induced by co-stimulation blockade. In this study, Tregs were essential for tolerance induction and their numbers increased over time. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19057 GPL16417
33 Samples
Download data: TAB
Series
Accession:
GSE220447
ID:
200220447
6.

Transcription and DNA Replication Shapes DNA Break Dynamics in Long Neuronal Genes

(Submitter supplied) Transcription and replication conflict (TRC) are one of the main driving forces for genome instability. Yet, TRC rarely been discussed without the context of DNA:RNA entanglement, rending the role of transcription in other TRC unclear . In neural stem and progenitor cells, genes encode protein regulating neuron adhesion are hotspots for recurrent DNA break clusters (RDC). While RDC-containing genes are all actively transcribed, most RDC lack DNA:RNA entanglement. more...
Organism:
Mus musculus
Type:
Other
Platforms:
GPL16417 GPL21626
79 Samples
Download data: BW, TLX
Series
Accession:
GSE233842
ID:
200233842
7.

eIF4G2 cross-linking immunoprecipitation (CLIP) in primary cortical neurons

(Submitter supplied) Learning and memory require activity-induced changes in mRNA translation within dendrites, but which mRNAs are involved and how they are regulated remain unclear. We combined proximity labeling with ribosome profiling and CLIP to monitor how depolarization impacts dendritic translation. For a functionally coherent set of transcripts highly enriched in mitochondrial genes, depolarization leads to enhanced uORF translation, eIF4G2 binding, and increased translation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16417
12 Samples
Download data: TXT
Series
Accession:
GSE213082
ID:
200213082
8.

Profiling data from primary mouse cortical neurons

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL16417 GPL24247
85 Samples
Download data: SF, TXT
Series
Accession:
GSE213083
ID:
200213083
9.

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
4 related Platforms
124 Samples
Download data: MCOOL, WIG
Series
Accession:
GSE234295
ID:
200234295
10.

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [SMF]

(Submitter supplied) Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediate these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes cause only moderate effects on the chromatin landscape, while removal of the NURF specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL16417
6 Samples
Download data: TXT
Series
Accession:
GSE234293
ID:
200234293
11.

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

(Submitter supplied) Gene expression is orchestrated by transcription factors (TFs), which bind to DNA in a sequence-specific manner, and by spatial genome structure, which constrains and shapes TF activity. Zinc finger protein 143 (ZNF143/ZFP143) is a TF that has been implicated in both gene activation and 3D genome organisation. We have generated an acute ZNF143/ZFP143 depletion system to study its direct consequences on chromatin looping and gene transcription. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL21626 GPL16417
57 Samples
Download data: BED, BW, HIC, MCOOL, TSV, TXT
Series
Accession:
GSE260914
ID:
200260914
12.

Experimental tests strongly challenge the evidence of a healthy human blood microbiome

(Submitter supplied) The study critically evaluate the results of 16S targeted amplicon sequencing performed on the total DNA collected from healthy donors’ blood samples in the light of specific negative controls.
Organism:
Mus musculus; human blood metagenome; Escherichia coli
Type:
Other
Platforms:
GPL34159 GPL16417 GPL16085
15 Samples
Download data: FASTA, TSV, TXT
Series
Accession:
GSE254843
ID:
200254843
13.

Age-associated chromatin re-organization in progenitor B cells

(Submitter supplied) Three-dimensional (3D) organization of the genome is essential for precise patterns of gene expression required for biological processes, however its role in physiological aging is not known.Here we show that large scale chromatin re-organization distinguishes bone marrow progenitor (pro-) B cells of old mice from that of young mice.These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs).One genomic region that transitions from compartment A to B with age contains the gene encoding Ebf1, a key regulator of normal B cell development.Genetically reducing Ebf1 recapitulates some features of old pro-B cells.TADs that are most reduced with age also harbor genes important for function and development of pro-B cells, including the immunoglobulin heavy chain (IgH) gene locus.Weaker intra-TAD interactions at IgH correlate with reduced utilization of distally located variable gene segments in VDJ recombination.Our observations implicate 3D chromatin re-organization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Genome variation profiling by high throughput sequencing
Platforms:
GPL16417 GPL24247 GPL19057
76 Samples
Download data: BED, BEDPE, TXT
Series
Accession:
GSE214438
ID:
200214438
14.

A ketogenic diet can revert acquired resistance to immunotherapy in prostate cancer through β-hydroxybutyrate-mediated inhibition of histone deacetylases

(Submitter supplied) Prostate cancer is the second leading cause of cancer deaths in men in the US. In the past decade, immune checkpoint blockade (ICB) drugs targeting programmed death 1 (PD-1) and cytotoxic T-lymphocyte antigen 4 (CTLA-4) have revolutionized the field of cancer therapeutics, but the objective response rate in prostate cancers is in the low single digits. A major complicating issue is that immunotherapies can have significant adverse effects, so there is a clinical need for novel combinatorial strategies that do not involve additional or compounding adverse effects. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL16417
6 Samples
Download data: CSV, MTX, TSV, TXT
Series
Accession:
GSE206561
ID:
200206561
15.

Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL24247 GPL16417
35 Samples
Download data
Series
Accession:
GSE248694
ID:
200248694
16.

Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells II

(Submitter supplied) The gut microbiota promotes immune system development in early life, but the interactions between the gut metabolome and immune cells in the neonatal gut remains largely undefined. Here, we demonstrate that the neonatal gut is uniquely enriched with neurotransmitters, including serotonin; specific gut bacteria produce serotonin directly while downregulating monoamine oxidase A to limit serotonin breakdown. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
19 Samples
Download data: XLSX
Series
Accession:
GSE248691
ID:
200248691
17.

Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells I

(Submitter supplied) The gut microbiota promotes immune system development in early life, but the interactions between the gut metabolome and immune cells in the neonatal gut remains largely undefined. Here, we demonstrate that the neonatal gut is uniquely enriched with neurotransmitters, including serotonin; specific gut bacteria produce serotonin directly while downregulating monoamine oxidase A to limit serotonin breakdown. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
8 Samples
Download data: XLSX
Series
Accession:
GSE248690
ID:
200248690
18.

Acute gastrointestinal permeability after traumatic brain injury in mice precedes a bloom in Akkermansia muciniphila supported by intestinal hypoxia

(Submitter supplied) Traumatic brain injury (TBI) initiates not only complex neurovascular and glial changes within the brain but also pathophysiological responses that extend beyond the central nervous system. The peripheral response to TBI has become an intensive area of research, as these systemic perturbations can induce dysfunction in multiple organ systems. As there are no approved therapeutics for TBI, it is imperative that we investigate the peripheral response to TBI to identify targets for future intervention. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
89 Samples
Download data: CSV, XLSX
Series
Accession:
GSE239472
ID:
200239472
19.

mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [KR158 RNA-TCR]

(Submitter supplied) mRNA-based immunotherapeutics have garnered widespread interest for their potential to revolutionize cancer treatment. In this study, we have established a personalized and customizable mRNA-therapeutic approach that effectively targets a plurality of tumor antigens and demonstrated potent anti-tumor response in preclinical brain tumor models. Our platform uniquely addresses the challenge of tumor heterogeneity and low antigen burden, two key deficiencies in targeting classically immunotherapy-resistant CNS malignancies.
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
9 Samples
Download data: TXT
Series
Accession:
GSE251800
ID:
200251800
20.

Id3 is required for the maintenance of tissue-infiltrating alloreactive T cells in GVHD but not anti-leukemia responses

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL24247 GPL16417
40 Samples
Download data: BEDGRAPH, H5
Series
Accession:
GSE230286
ID:
200230286
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