GSE263741 Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain
In this study, we attempted to study AID-mediated mutations of TBLV proviruses lacking Rem expression obtained from tumors in C57BL/6 (B6) wild-type and AID-knockout backgrounds. Surprisingly, no differences in G-to-A mutations were observed in TBLV proviruses regardless of Rem expression, yet such mutations were significantly reduced in proviruses obtained from mA3/AID-double knockout mice relative to those from wild-type B6 or AID-knockout mice. Many cellular mRNAs involving the innate immune response, but not Apobecs, were elevated in the absence relative to the presence of Rem expression on the B6 AID-knockout backgrou...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research
GSE263751 PEX5 integrates p38 MAPK signaling pathway and taurine metabolism to regulate cellular senescence in lung fibroblasts
Contributors : Lingjun Zheng ; Xiaoqin Yang ; Xiong SuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lung diseases significantly impact the aging population globally, but their etiology is largely unknown, and the therapeutic options are minimal. Cellular senescence has been increasingly recognized as an essential driving mechanism for chronic lung diseases. Remodeling in subcellular compartments is commonly observed in senescent cells, which reciprocally regulates the senescent progression. Roles of peroxisomes in cellular senescence have been documented, but the molecula...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE263764 Effect of splenectomy on liver regeneration after 70% resection in a mouse model.
Contributor : Andrey ElchaninovSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn this work, the effect of splenectomy on liver regeneration was studied. For this purpose in 1 series of experiments the animals were reproduced splenectomy, and after 7 days 70% liver resection was performed. It was found that spleen removal leads to a decrease in the migration of Ly6C+ monocytes into the regenerating liver. Using transcriptional analysis it was shown that spleen and peripheral blood monocytes differ in the expression of genes associated with the synthesis of surface receptors necessary...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE263852 Linc-ADAIN, A Human Adipose LincRNA Regulates Adipogenesis by Modulating KLF5 and IL-8 mRNA stability
Contributors : Marcella E O'Reilly ; Chenyi Xue ; Eunyoung KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAdipose tissue remodeling and dysfunction, characterized by increased inflammation and insulin resistance, play a central role in obesity-related development of type 2 diabetes (T2DM) and cardiovascular diseases. Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular functions. Here we describe the functions of linc-ADAIN (ADipose Anti-INflammatory), an adipose lincRNA that is downregulated in white adipose tissue of obese humans. We demonstrate that...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE263858 Transcriptomic analysis of C. elegans mutants which do not respond to oomycete exposure
Contributors : Kenneth Liu ; Manish Grover ; Michalis BarkoulasSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansWe have established epidermal expression of chil-27p::GFP as the marker for activation of oomycete recognition response (ORR) in C. elegans. Through a forward genetic screen, we identified clec-27, clec-35, and ceh-37 to be the key players required for activating chil-27p::GFP upon exposure to the oomycete Myzocytiopsis humicola extract. To determine if activation of entire ORR is affected in these mutants, we analyzed their transcriptome in the presence and abse...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research
GSE263914 Regulation of Microprocessor assembly and localization via Pasha ’s WW domain in C. elegans
Contributor : Taiowa A MontgomerySeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Caenorhabditis elegansPrimary microRNA (pri-miRNA) transcripts are processed by a protein complex called the Microprocessor comprised of the ribonuclease Drosha and its RNA binding partner DGCR8/Pasha. We sequenced small RNAs from animals containing a mutation in the WW domain of C. elegans pash-1. We found that these mutants have a modest but widespread reduction in miRNA levels when grown at 20 ˚C, which is further enhanced when grown at 25˚C. The results demonstrate a requirement for the WW domain in process...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Caenorhabditis elegans Source Type: research
GSE263946 Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy [RNA-seq]
Contributors : Lays M Sobral ; Faye Walker ; Etienne Danis ; Nathan DahlSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensUsing a combination of ChIP-, ATAC-, RNA-seq, and CUT&RUN in model systems of diffuse intrinsic pontine glioma and other pediatric high-grade gliomas, we observe a rapid genome-wide reorganization of active chromatin within hours of exposure to therapeutic ionizing radiation. This redistribution facilitates PTEFb-mediated pause-release of Pol II to drive nascent transcriptional induction of canonical DNA damage response programs. Concurrent inhibition of PTEFb imp...
Source: GEO: Gene Expression Omnibus - April 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE263857 Effects of a humanized ectopic niche (human ossicle or hOss) on human hematopoiesis
Contributors : Laurent Renou ; Wenjie Sun ; Chlo é Friedrich ; Klaudia Galant ; Cécile Conrad ; Evelia Plantier ; Katharina Schallmoser ; Linda Krisch ; Vilma Barroca ; Saryami Devanand ; Nathalie Déchamp ; Andréas Reinisch ; Jéléna Martinovitch ; Alessandra Magnani ; Lionel Faivre ; Julien Calvo ; Leila Perié ; Olivier Kosm ider ; Françoise PflumioSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman hematopoiesis takes place in the bone marrow (BM) where a multitude of interactions regulate differentiation and preservation of hematopoietic stem/progenitor ...
Source: GEO: Gene Expression Omnibus - April 15, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE99979 Recognition of a pediatric glioblastoma-associated histone mutation by chromatin reader ZMYND8 promotes tumorigenesis
Contributors : Rui Guo ; Yang ShiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHistone H3 point mutations have recently been identified in pediatric brain cancers, including missense mutations on histone H3 at positions 27 (lysine to methionine; K27M) and 34 (glycine to arginine, G34R), respectively. H3K27M mutations are associated with a majority of pediatric Diffuse Intrinsic Pontine Pediatric Glioma (DIPG) cases, while H3.3G34R is found in pediatric glioblastoma (GBM) arising in the cerebral cortex1,2. While the mechanisms of H3K27M-driven tumorigenesis are beginn...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE172150 Expression of miRNA in exosomes from transudative pleural effusion and tuberculous pleural effusions
Contributors : Li-Mei Liang ; Meng Wang ; Hong Ye ; Wan-Li MaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensPleural fibrosis is defined as an excessive deposition of extracellular matrix (ECM) that results in destruction of the normal pleural tissue architecture and compromised function. However there is currently no effective medication for pleural fibrosis. Understanding the detailed mechanisms of pleural fibrosis is an important unmet need which could lead to the identification of new targets for treatment of this condition. microRNAs (miRNAs) play an important role in th...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research
GSE215901 SPATAC-seq: split-pool ligation-based single cell ATAC-seq method
Contributors : Keyong Sun ; Xun LanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusTo establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. Briefly, in SPATAC-seq, (1) fixed nuclei are transposed in 48 ...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research
GSE216371 A single-cell atlas of chromatin accessibility in mouse organogenesis
Contributors : Keyong Sun ; Xun LanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusRecent surveys of mouse organogenesis cell atlas (MOCA) with single cell transcriptomics have uncovered hundreds of cell types, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each cell type have yet to be elucidated. We applied a four-level combinatorial indexing assay, SPATAC-seq, to profile the chromatin accessibility in>350,000 cells derived from 13 embryos staged between embryonic day (E) 10.5 and 13.5 in a single e...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE229796 Effect of electroacupuncture on gene expression of adipose tissue in HFD-induced obese mice
Contributors : Hongyan Gao ; Yanhui LiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate whether electroacupuncture (EA) promotes adipose tissue browning by regulating the expression of angiogenesis genes through EA, we sequenced the adipose tissue of mice fed high fat diet with and without electroacupuncture, as well as those fed normally.We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 mice in three groups. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE239468 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [ChIP-seq and CUT & Tag]
Contributors : Liling Wan ; Yiman Liu ; Qinglan LiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusGain-of-function mutations in the chromatin ‘reader’ ENL, identified in AML and Wilms tumor, have been shown to induce aberrant formation of transcriptional condensates in cellular systems. However, the precise role of these mutations and their condensate forming property in tumorigenesis remains unclear. By creating a conditional knock-i n mouse model for the most prevalent ENL mutation, we establish ENL mutant as a bona fide oncogenic driver of acute myeloid leukemi...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE239469 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [RNA-seq]
Contributors : Liling Wan ; Yiman Liu ; Qinglan LiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGain-of-function mutations in the chromatin ‘reader’ ENL, identified in AML and Wilms tumor, have been shown to induce aberrant formation of transcriptional condensates in cellular systems. However, the precise role of these mutations and their condensate forming property in tumorigenesis remains unclear. By creating a conditional knock-i n mouse model for the most prevalent ENL mutation, we establish ENL mutant as a bona fide oncogenic driver of acute myeloid leukemia in vivo. Het...
Source: GEO: Gene Expression Omnibus - April 14, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
