GSE254691 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT & RUN]
Contributors : Xiaoyi G Liang ; Kendy Hoang ; Yue Zhang ; Sol Katzman ; Bin ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDuring development neural stem cells (NSCs) in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Shh ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE254692 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT & RUN 22]
Contributors : Xiaoyi G Liang ; Kendy Hoang ; Yue Zhang ; Sol Katzman ; Bin ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDuring development neural stem cells (NSCs) in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Shh ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE265958 Deletion of an sRNA primes development in a multicellular bacterium
Contributors : Marco La Fortezza ; Jasper Verwilt ; Sarah Cossey ; Sabrina Eisner ; Gregory J Velicer ; Yuen-Tsu Nicco YuSeries Type : Expression profiling by high throughput sequencingOrganism : Myxococcus xanthusSmall non-coding RNAs (sRNAs) are essential in regulating gene expression during many biological processes. In myxobacteria, the gene pxr encodes for an sRNA known to block the activation of fruiting body development, an aggregative multicellular process triggered by starvation. However, a comprehensive list of potential targets of Pxr and whether these are indeed associated with development still needs to b...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Myxococcus xanthus Source Type: research
GSE265991 Pien Tze Huang enhances the killing effect of autologous T cells in colorectal cancer by inhibiting PD-L1, stem cell markers, and STAT3.
Conclusion: PZH enhances T cell-mediated killing effect by inhibiting CRC stem cell markers, PD-L1, and STAT3. Key Words: Pien Tze Huang, patient-derived organoid, colorectal cancer stem cells, programmed death protein ligand-1, signal transducer and activator of transcription 3 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE266047 Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [bulkRNA-seq]
In this study, we examine the effect of radiation on the transcriptional profile of medulloblastoma tumor cells and its microenvironment that could potentially be leading to metastatic dissemination. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE266048 Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [scRNA-seq]
In this study, we examine the effect of radiation on the transcriptional profile of medulloblastoma tumor cells and its microenvironment that could potentially be leading to metastatic dissemination. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE266121 N6-Methyladenosine RNA Modification Regulates the Differential Muscle Development in Large White and Ningxiang Pigs
In this study, we identified differentially expressed genes in the early stages of muscle development between Large White (LW) and NingXiang (NX) pigs and further reported m6A methylation patterns via MeRIP-seq. We found that m6A modification regulates muscle cell development, myofibrils, cell cycle, and phosphatase regulator activity during the neonatal phase of muscle development. Interestingly, differentially expressed genes in LW and NX pigs were mainly enriched in pathways involved in protein synthesis. Furthermore, we performed a conjoint analysis of MeRIP-seq and RNA-seq data, and identified 27 differentially expres...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Sus scrofa Source Type: research
GSE266268 ENL reads histone β-hydroxybutyrylation to modulate gene transcription (CUT & Tag)
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHistone modifications are typically recognized by chromatin-binding protein modules (referred to as “readers”) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap must be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research
GSE266269 ENL reads histone β-hydroxybutyrylation to modulate gene transcription (RNA-Seq)
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHistone modifications are typically recognized by chromatin-binding protein modules (referred to as “readers”) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap must be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE254689 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [ATAC-seq]
Contributors : Xiaoyi G Liang ; Kendy Hoang ; Yue Zhang ; Sol Katzman ; Bin ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDuring development neural stem cells (NSCs) in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Shh ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE254658 Six1 regulates mouse lower incisor development by coordinating Dlx1/2/5 [scRNA-seq]
This study employs Six1 deletion mouse models to elucidate the critical regulatory role of Six1 in governing dental mesenchyme development. By performing single-cell RNA sequencing (scRNA-seq), we constructed a comprehensive transcriptome atlas of tooth germ development from the bud to bell stage. Our analyses suggest that the dental follicle (DF) and the dental papilla (DP) are differentiated from dental ectomesenchyme (DEM), and identify the key transcription factors (TFs) underlying these distinct states. Notably, we show that Dlx1, Dlx2, and Dlx5 (Dlx1/2/5) may function as the key TFs that promote the formation of DP. ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE254482 Six1 regulates mouse lower incisor development by coordinating Dlx1/2/5 [CUT & Tag]
This study employs Six1 deletion mouse models to elucidate the critical regulatory role of Six1 in governing dental mesenchyme development. By performing single-cell RNA sequencing (scRNA-seq), we constructed a comprehensive transcriptome atlas of tooth germ development from the bud to bell stage. Our analyses suggest that the dental follicle (DF) and the dental papilla (DP) are differentiated from dental ectomesenchyme (DEM), and identify the key transcription factors (TFs) underlying these distinct states. Notably, we show that Dlx1, Dlx2, and Dlx5 (Dlx1/2/5) may function as the key TFs that promote the formation of DP. ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research
GSE246851 The evolutionarily conserved zebrafish choroid plexus maintains the size of brain ventricles
Contributors : Jeong Inyoung ; Jurisch-Yaksi NathalieSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe choroid plexus produces cerebrospinal fluid (CSF) by transport of electrolytes and water from the vasculature to the brain ventricles. The choroid plexus plays additional roles in brain development and homeostasis by secreting neurotrophic molecules, and by serving as a CSF-blood barrier and immune interface. Prior studies have identified transporters on the epithelial cells that transport water and ions into the ventricles and tight junctions involved in the CSF-blood barrier. Ye...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research
GSE243982 Deciphering bat influenza H18N11 infection dynamics in Jamaican fruit bats on a single cell level
Contributors : Geoffroy Andrieux ; Melanie Boerries ; Kevin Ciminski ; Susanne Kessler ; Tony SchountzSeries Type : Expression profiling by high throughput sequencingOrganism : Artibeus jamaicensisJamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected Jamaican fruit bats with the bat-derived influenza A virus H18N11. Using comparative single-cell RNA sequencing, we generated a single-cell atlas ...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Artibeus jamaicensis Source Type: research
GSE232630 Dnmt3a1 regulates memory formation via the downstram target Nrp1
In this study, we investigated the requirement for Dnmt3a1, the predominant Dnmt in the adult brain, in hippocampal long-term memory formation. Furthermore, we identified an activity-regulated Dnmt3a1-dependent genomic program. Our data showed that Dnmt3a1, similarly to its isoform Dnmt3a2, plays a critical role in memory formation. Furthermore, we uncovered Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 during the formation of memory. Intriguingly, we found that Nrp1 expression is selectively regulated and a specific downstream effector of Dnmt3a1, but not Dnmt3a2. Taken together, our study uncovered a Dnmt3a isofo...
Source: GEO: Gene Expression Omnibus - May 6, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
