GSE226838 Profiling the neuroimmune cascade in 3xTg mice exposed to successive mild traumatic brain injuries
Contributors : Levi B Wood ; Alyssa F Pybus ; Sara Bitarafan ; Erin M BuckleySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRepetitive mild traumatic brain injuries (rmTBI) sustained within a window of vulnerability can result in long term cognitive deficits, depression, and eventual neurodegeneration associated with tau pathology, amyloid beta plaques, gliosis, and neuronal and functional loss. However, we have limited understanding of how successive injuries affect the brain to result in these devastating long-term consequences. In the current study, we addressed the question of h...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE227043 Transcriptome profiling of multi-chambered stomachs in developing lambs [Day 5 and 10]
Contributors : B Yang ; K Huang ; H Chen ; J WangSeries Type : Expression profiling by high throughput sequencingOrganism : Ovis ariesWe perform transcriptomic sequencing of rumen, reticulum, omasum, and abomasum epithelial tissues from developing lambs.We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points (day5 and day10). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Ovis aries Source Type: research

GSE229259 Ambient RNA analysis of cortex-specific single-nuclei RNA-Seq (snRNA-seq) data in the sham and bilateral carotid artery stenosis (BCAS) groups
Contributor : Yuan ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWhen compared with the sham group, ambient RNAs were more predominant in the BCAS group, which originated from damaged neuronal nuclei. After CellBender and subcluster cleaning treatments, detectable ambient RNA contamination could be largely reduced, and cortex-specific transcriptomic maps in the sham and BCAS groups were generated successfully.The underlying cellular and molecular mechanisms related to cortex damage and glial activation after severe cerebral hypoperfusion were further investigated at single nuc...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE230138 Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3 [Affymetrix]
In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells aft...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE230141 Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3 [ChIPseq]
In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells aft...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE230142 Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3
Series Type : Expression profiling by array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE230162 Glutamine antagonist JHU083 reprograms immunosuppressive tumor-associated macrophages to drive tumor immunity in urologic cancer
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE230237 Generation of immune-enhancing neutrophils by subclinical super-low dose LPS
Contributors : Yao Zhang ; Ziyue YI ; Shuo Geng ; Liwu LiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe have generated immune-enhancing neutrophils by culturing murine primary bone marrow derived neutrophils with either super-low dose of LPS. Immune-enhancing neutrophils preferentially express co-stimulatory molecules such as CD74, CD44 and CD86, and exhibit reduced expression of CD11b. Purified bone marrow neutrophils were treated with PBS or 100 pg/ml LPS overnight in the presence of GM-CSF, and harvested for scRNAseq analysis to examine their profiles of gene expression. (...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE232147 Loss of RUNX1 favors mesenchymal stem cells development at the expense of hematopoiesis in hPSC-derived hematopoiesis
Contributors : Cuihua Wang ; Igor M SamokhvalovSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOur data demonstrated an unprecedented role of RUNX1 in regulating hematopoietic and mesenchymal fate decisions in human pluripotent stem cells (hPSC)-derived hematopoiesis (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE232166 Dual AAV gene therapy in combination with rapamycin rescues muscle and liver impairment in a mouse model of GSDIII.
In conclusion, these results indicate that correction of both liver and muscle can be achieved in symptomatic GSDIII mice by an overlapping vector expressing GDE with a tandem promoter when combined with rapamycin treatment. These data also indicate that the effect of rapamycin on AAV gene transfer although disease- and tissue-specific has a net positive impact on dual AAV gene therapy for GSDIII thus opening the way to the clinical translation of this combination approach. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE232408 Biomarkers to Measure Treatment Response for Alcohol Dependence
Contributors : Chamindi Seneviratne ; Suvarna Nadendla ; Jain Aluvathingal ; Nastaran Badrzadeh ; Amol C Shetty ; Xin-Qun Wang ; Jessica Cornell ; John Sivinski ; Maureen Kane ; Nageshwara Pilli ; Lisa SadzewiczSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study was to identify molecular mechanisms regulated by pharmacological and placebo effects of binge-drinking at a transcriptome-wide level. We performed RNA-seq on PBMC samples collected from healthy heavy social drinkers (N=18) enrolled in an upto 12-day in-patient, randomized, double-blind, cross-over...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE236258 Trametinib sensitizes KRAS-mutant lung adenocarcinoma tumors to PD-1/PD-L1 axis blockade via Id1 downregulation
Conclusions: Our data may support the role of Id1 in the trametinib antitumoral effect, sustaining the mitogen-activated protein kinases (MAPK) signaling pathway involved in the trametinib acquired resistance cells and sensitizing KRAS-mutant lung tumors to PD-1 inhibitors, through PD-L1 overexpression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE236621 SH-SY5Y human neuronal cells with mutation of the CDKN2B-AS1 gene are vulnerable under cultured conditions
Contributors : Michiko Ohno-Oishi ; Zou Meiai ; Kota Sato ; Seiya Kanno ; Chihiro Kawano ; Makoto Ishikawa ; Toru NakazawaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe show that gene expression change of CDKN2B-AS1 overexpressed SH-SY5Y neuroblastoma cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE237697 Increased activity of protein kinase A, even without DNAJB1, is sufficient to cause Fibrolamellar hepatocellular carcinoma
Contributors : David Requena ; Mahsa Shirani ; Ype P deJong ; Sanford M SimonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMost fibrolamellar carcinoma (FLC) is driven by a fusion of DNAJB1 and PRKACA, the catalytic subunit of protein kinase A (PKA). Overexpression of DNAJB1::PRKACA, ATP1B1::PRKACA or PRKACA, but not catalytically inactive kinase, caused similar transcriptomic changes of primary human hepatocytes; these recapitulated most changes observed in FLC. This is consistent with the observation that FLC is found in patients missing a regulatory subunit or with a ATP1B1::PR...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE237792 Transcriptome analysis of VapC13 and VapC26 overexpression in Mycobacterium tuberculosis
We report the effects of VapC13 and VapC26 overexpression on the transcriptome of M. tuberculosis. For RNA-seq experiments, early-log phase cultures (OD600nm ~ 0.2-0.3) of M. tuberculosis strains harboring either pTetR or pTetR-vapC13 or pTetR-vapC26 were induced with the addition of 50 ng/ml Atc for 24 h. For total RNA isolation, induced cultures were harvested by centrifugation, washed twice with 1x PBS and lysed by bead beating in Trizol. Total RNA was extracted by phenol-chloroform, precipitated with isopropanol and eluted using Qiagen RNA isolation kit as per manufacturer ’s instructions. We report that VapC13 or Va...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mycobacterium tuberculosis H37Rv Source Type: research