GSE199297 RNA-seq of Phytophthora infestans T30-4 two infection stages
Contributors : Han Chen ; Haidong ShuSeries Type : Expression profiling by high throughput sequencingOrganism : Phytophthora infestansPhytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histon...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Phytophthora infestans Source Type: research

GSE199298 Epigenetic states in P. infestans
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Phytophthora infestansThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Phytophthora infestans Source Type: research

GSE205229 Isthmal stem cells sustain intestinal homeostasis and regeneration
Contributors : Ermanno Malagola ; Alessandro Vasciaveo ; Andrea Califano ; Timothy C WangSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe currently accepted intestinal epithelial cell organization model equates crypt base columnar (CBC) cells, marked by high levels of Lgr5 expression, with the intestinal stem cell (ISC). However, recent intestinal regeneration studies have uncovered limitations of the ‘Lgr5-CBC’ model, leading to two major views: one favoring the presence of a quiescent reserve stem cell popu...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE216734 Gene expression profiles of chimeric cytokine receptor-engineered CAR-T cells
In this study, we developed a chimeric cytokine receptor composed of the extracellular domains of GP130 and IL6RA linked to the transmembrane and cytoplasmic domain of IL-7R mutant that constitutively activate JAK-STAT pathway (G6/7R). CAR-T cells with G6/7R efficiently absorbed and degraded monocyte-derived IL-6 both in vitro and in vivo. The G6/7R-expressing CAR-T cells showed superior expansion and persistence in vivo, which resulted in durable antitumor response in multple tumor models. Our strategy can be widely applicable to CAR-T cell therapy to enhance its efficacy and safety, irrespective of the target antigen. (S...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE228143 Gene expression of A549 cells after cocultured with Trichomonas tenax
Contributor : Wei-Chen LinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the gene expression of lung epithelial cells effected by Trichomonas tenax, we chose A549 lung epithelial cells and cocultured with Trichomonas tenax at MOI1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE228191 Gene expression profile at single cell level of Wild type and Plagl1 knock out retina at P7
Contributors : Yacine Touahri ; Chao Wang ; Carol SchuurmansSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPlagl1 controls Muller glial cells proliferation in the retina. We used single cell RNA sequencing (scRNA-seq) to analyze the prolirative state of Muller glial cells and identify the signals that might be involved in this process (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE228216 Gene expression of NCI-H292 cells after cocultured with Trichomonas tenax
Contributor : Wei-Chen LinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the gene expression of lung epithelial cells effected by Trichomonas tenax, we chose NCI-H292 lung epithelial cells and cocultured with Trichomonas tenax. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE228266 CRISPRTE: A web-based tool to generate single guide RNA targets transposable elements
Contributors : Yixinguo Guo ; Wanlu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been develope...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE228918 Transcriptome dynamics of mutualistic poxvirus infection of tropical fruit fly hosts
In this study, we investigated the role of a mutualistic poxvirus in shaping the host range of D. longicaudata across three genera of agricultural pest species: two of which are permissive hosts for D. longicaudata parasitism and one that is a nonpermissive host. We found that permissive hosts Ceratitis capitata and Bactrocera dorsalis were highly susceptible to virus infection, displaying rapid virus replication and abundant fly mortality. However, the nonpermissive host Zeugodacus cucurbitae largely overcame virus infection, exhibiting substantially lower mortality and no virus replication. Further investigation of trans...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bactrocera dorsalis Ceratitis capitata Zeugodacus cucurbitae Source Type: research

GSE236785 FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [ATAC-Seq]
Contributors : Roberta Migale ; Michelle Neumann ; Mahmoud-Reza Rafiee ; Sophie Wood ; Jessica Olsen ; Robin Lovell-BadgeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusFOXL2 is a transcription factor essential for female fertility, expressed in somatic cells of the ovary, notably granulosa cells. In the mouse, Foxl2 deletion leads to partial sex reversal postnatally, with mutants developing dysgenic ovaries devoid of oocytes. However, deletion of the gene in 8-week-old females leads to granulosa to Sertoli cell transdifferentiation and gonadal sex reversal. We hyp...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE236859 FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [RNA-Seq]
Contributors : Roberta Migale ; Michelle Neumann ; Mahmoud-Reza Rafiee ; Sophie Wood ; Jessica Olsen ; Robin Lovell-BadgeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFOXL2 is a transcription factor essential for female fertility, expressed in somatic cells of the ovary, notably granulosa cells. In the mouse, Foxl2 deletion leads to partial sex reversal postnatally, with mutants developing dysgenic ovaries devoid of oocytes. However, deletion of the gene in 8-week-old females leads to granulosa to Sertoli cell transdifferentiation and gonadal sex reversal. We hypothesise that ...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE236860 FOXL2 interaction with different binding partners regulates the dynamics of granulosa cell differentiation across ovarian development [ChIP-Seq]
Contributors : Roberta Migale ; Michelle Neumann ; Mahmoud-Reza Rafiee ; Sophie Wood ; Jessica Olsen ; Robin Lovell-BadgeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusFOXL2 is a transcription factor essential for female fertility, expressed in somatic cells of the ovary, notably granulosa cells. In the mouse, Foxl2 deletion leads to partial sex reversal postnatally, with mutants developing dysgenic ovaries devoid of oocytes. However, deletion of the gene in 8-week-old females leads to granulosa to Sertoli cell transdifferentiation and gonadal sex reversal. We hyp...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE236862 FOXL2 interaction with different binding partners regulates the dynamics of ovarian development
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThe transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2 ’s role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on chr...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE246624 Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing
In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE255145 Gene expression profiles of CAR-T cells engineered with chimeric cytokine receptors to induce JAK-STAT signaling
In this study, we developed a chimeric cytokine receptor consisting of the extracellular domains of GP130 and IL6RA linked to the transmembrane and cytoplasmic domain of IL-7R mutant (insertion of PPCL) (G6/7R). We also generated a modified receptor with the M452L mutation in the IL7R cytoplasmic domain (G6/7R-M452L). CAR-T cells with G6/7R or G6/7R-M452L efficiently absorbed monocyte-derived IL-6 and induced a superior therapeutic response compared to conventional CAR-T cells. Our strategy can be broadly applied to CAR-T cell therapy to enhance its efficacy and safety, irrespective of the target antigen. (Source: GEO: Gen...
Source: GEO: Gene Expression Omnibus - March 24, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research