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Gene Expression Omnibus Announcements & Study Releases
Announcements of updates and changes to the Gene Expression Omnibus (GEO) databases and notifications of newly released functional genomic studies.
- GSE270120 Genome-wide profiling of R-loop by affinity-independent and nuclease-based method [RIAN-seq] March 18, 2025Series Type : Other ; Methylation profiling by high throughput sequencingOrganism : Homo sapiens ; Saccharomyces cerevisiae S288CR-loop is abundant triplex nucleic strand in organism, but many physiological and pathological functions remain to be fully understood, owing to a lack of robust and high-resolution methods for genome-wide detection. In this study, […]
- GSE262790 Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos March 18, 2025Contributors : Tsunetoshi Nakatani ; Tamas Schauer ; Maria-Elena Torres-PadillaSeries Type : OtherOrganism : Mus musculusRepli-seq datasets were generated using single cell Repli-seq as described in Nakatani et al. (2024). Embryos were microinjected with an siRNA control or an siRNA against Rif1 at the zygote stage. Individual cells were collected for scRepl […]
- GSE244247 Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells [RNA-seq] March 18, 2025Contributors : Anastasia Conti ; Stefano Beretta ; Kety Giannetti ; Teresa Tavella ; Ivan Merelli ; Raffaella Di MiccoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGene editing (GE) using homology-directed repair (HDR) in hematopoietic stem and progenitor cells (HSPCs) offers promise for long-range gene correction of […]
- GSE198962 RNA sequencing of normal and unilateral ureteral obstruction (UUO) operated mouse kidneys March 18, 2025Contributors : Andrew Advani ; Harmandeep KaurSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA-sequencing of mouse left kidneys for which the left ureter was obstructed (UUO) or not obstructed (sham) animals, isolated 14 days after the surgery
- GSE260793 Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (ChIP-Seq) March 18, 2025Contributors : Jing Zhang ; Chuan GaoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHypoxia and dysregulation of three-dimensional (3D) chromatin architecture can both activate oncogenic transcriptomic profiles, thus contributing to tumor malignancy. But how hypoxia regulates 3D chromatin architecture rem […]
- GSE254469 Affinity-independent and nuclease-based strategy to profile R-loop genome-wide [mESC] March 18, 2025Contributors : Yaoyi Li ; Yingliang Sheng ; Hongjie YaoSeries Type : OtherOrganism : Mus musculusR-loop is abundant triplex nucleic strand in organism, but many physiological and pathological functions remain to be fully understood, owing to a lack of robust and high-resolution methods for genome-wide detection. In this study, we develop R-loop identificatio […]
- GSE291915 The Hira complex regulates Gli3R-dependent transcription in Hedgehog signaling and medulloblastoma cell growth and migration [RNA-seq] March 18, 2025Contributors : Weronika Skarzynska ; Brygida Baran ; Pawel NiewiadomskiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRegulation of the Hedgehog pathway activity may be supported by coactivators and corepresors of its main effectors- Gli transcription factors. While activation processes are well studied, repression mec […]
- GSE261843 CARM1 inhibits ferroptosis in bladder cancer cells by upregulating the expression of ENO1 March 18, 2025Contributors : Yuqi Tang ; Weimin Hu ; Ming Li ; Linzhi Li ; Yunlong Zhang ; Jinzhuo Ning ; Fan ChengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCoactivator-associated arginine methyltransferase 1 (CARM1) is a protein that helps regulate gene expression. Research has shown that CARM1 is also involved in autophagy, R […]
- GSE292040 Direct cell-to-cell transmission of retrotransposons [Minion] March 18, 2025Contributors : Maya Voichek ; Andreas Bernhard ; Maria Novatchkova ; Dominik Handler ; Paul Möseneder ; Baptiste Rafanel ; Peter Duchek ; Kirsten-André Senti ; Julius BrenneckeSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTransposable elements are abundant in host genomes but are generally considered to be […]
- GSE291945 The Hira complex regulates Gli3R-dependent transcription in Hedgehog signaling and medulloblastoma cell growth and migration March 18, 2025Contributors : Weronika Skarzynska ; Brygida Baran ; Pawek NiewiadomskiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusRegulation of the Hedgehog pathway activity may be supported by coactivators and corepresors of its main effectors- Gli transcription factors. While activation processes are well studied, […]
- GSE292041 Direct cell-to-cell transmission of retrotransposons [RNA-seq] March 18, 2025Contributors : Maya Voichek ; Andreas Bernhard ; Maria Novatchkova ; Dominik Handler ; Paul Möseneder ; Baptiste Rafanel ; Peter Duchek ; Kirsten-André Senti ; Julius BrenneckeSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTransposable elements are abundant in host genomes but are generally considered to be […]
- GSE292043 A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum March 18, 2025Contributors : Jens B Christensen ; Alex Donovan ; Andrea H Brand ; Sumru BayinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusUnderstanding the molecular mechanisms driving lineage decisions and differentiation during development is especially difficult in systems with a diverse progenitor pool, such as t […]
- GSE292044 Direct cell-to-cell transmission of retrotransposons March 18, 2025Contributors : Maya Voichek ; Andreas Bernhard ; Maria Novatchkova ; Dominik Handler ; Paul Möseneder ; Baptiste Rafanel ; Peter Duchek ; Kirsten-André Senti ; Julius BrenneckeSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Drosophila melanogasterTransposable elements are abundant in host genomes but are generally considered to […]
- GSE262788 LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos March 18, 2025Contributors : Mrinmoy Pal ; Tsunetoshi Nakatani ; Tamas Schauer ; Maria-Elena Torres-PadillaSeries Type : OtherOrganism : Mus musculusWe investigated how RIF1 depletion affects the nuclear organization in mouse preimplantation embryos by performing DamID-seq to map lamina-associated domains (LADs).
- GSE291904 Polystyrene microplastics induce activation and cell death of neutrophils through strong adherence and engulfment March 18, 2025Contributors : Koung-Min Park ; Bora Kim ; Wonjin Woo ; Lark Kyun Kim ; Young-Min HyunSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIngested microplastics (MPs) can accumulate throughout whole body, which may induce the dysfunction of immune system. However, it remains unclear how MP exposure affects innate immune res […]