NCBI GEO2026 · Excel spreadsheet · 14 samples
Novel B cell deficiency [CITE-seq]We identified 5 patients from two families with a defect in antibody production without a known inborn error of immunity.
NCBI GEO2026 · Table · CSV · 2 samples
IMiD/CELMoD resistance in myeloma is associated with changes in lipid metabolism that may be targetableImmunomodulatory drugs (IMiDs) are a cornerstone of multiple myeloma treatment and newer cereblon E3 ligase modulating drugs (CELMoDs) are in clinical trials. However, a major barrier to improving patient outcomes is the inevitable development of resistance to these agents. To explore the mechanisms underlying IMiD/CELMoD resistance, and identify novel targets for treatment, human cell line models
NCBI GEO2026 · RNA sequencing · 14 samples
APOE4 disrupts the central dogma by arresting neuronal proteome dynamicsApolipoprotein E4 (APOE4), the strongest genetic risk factor for late-onset Alzheimer's disease, promotes neuronal dysfunction through incompletely understood mechanisms. Here, we integrated transcriptomic, translatomic, and proteomic profiling of isogenic human iPSC-derived APOE3 and APOE4 neurons and found that APOE4 fundamentally impairs neuronal proteome renewal. Although transcriptional chang
NCBI GEO2026 · Raster · GeoTIFF · 3 samples
A molecular and spinal circuit basis for the functional segregation of itch and painThe dorsal horn is remarkably diverse, yet how this cellular complexity enables discrimination of sensory modalities remains a fundamental question. Neurons expressing gastrin-releasing peptide receptor (Grpr+) have long been considered dedicated to itch, yet broad activation also evokes pain-related behavior. Whether Grpr+ neurons are required for pain, and how itch- and pain-related functions ar
NCBI GEO2026 · RNA sequencing · 50 samples
Antigen-Specific Hhexhigh CD4+ effectors as bona fide precursors of memory TFH cells to safeguard long-term humoral immunityThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Sequencing data · 8 samples
Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers [other]Although mutations in genes encoding histones display a similar prevalence to that of some other somatic mutations in cancer, the underlying mechanisms by which histone mutations drive tumorigenesis have not been fully explored. Herein, we curated missense mutations occurring in core histone genes in breast cancers using data from MSK-IMPACT and cBioPortal to identify high frequency breast cancer-
NCBI GEO2026 · study · 8 samples
Influence of histone acetylation on chromatin 3D organization in Drosophila S2 cells [HiC]Alterations in histone acetylation are frequently detected in various cancers and upon neurological deseases. The histone acetylation is known to disrupt both intra- and inter-nucleosomal interactions. However, its influence on the higher order chromatin organization has been studied to a lesser extent. In this study, we changed global levels of histone acetylation in Drosophila S2 cells by treatm
NCBI GEO2026 · Excel spreadsheet · 12 samples
Transcriptome-wide m6A RNA methylation profiling in parental and enzalutamide-resistant C4-2 prostate cancer cellsThis study investigates transcriptome-wide N6-methyladenosine (m6A) RNA methylation profiles in parental and enzalutamide-resistant C4-2 prostate cancer cells using methylated RNA immunoprecipitation sequencing (MeRIP-seq).
NCBI GEO2026 · Text · 2 samples
ELAC1 selectively trims vault RNA 3′ ends, revealing substrate partitioning between human RNase Z paralogsRibonuclease Z enzymes remove 3′ trailers from precursor tRNAs. In human cells, ELAC2/RNase ZL matures nuclear and mitochondrial pre-tRNAs and releases the tRNA-like small RNAs mascRNA and menRNA from the 3′ ends of MALAT1 and NEAT1. Instead, the cytosolic short paralog ELAC1/RNase ZS repairs ANKZF1-cleaved tRNAs, with its wider substrate repertoire remaining unresolved. Here, we investigate the r
NCBI GEO2026 · Table · CSV · 42 samples
Novel B cell deficiency [BCR-seq]We identified 5 patients from two families with a defect in antibody production without a known inborn error of immunity.
NCBI GEO2026 · study · 4 samples
Influence of histone acetylation on genome architecture in Drosophila S2 cellsHistone acetylation is known to disrupt both intra- and inter-nucleosomal interactions, but its influence on higher-order chromatin organization has been studied to a lesser extent. In this study, we changed global levels of histone acetylation in Drosophila S2 cells by knock-down of the main histone deacetylase HDAC1/Rpd3 in S2 cells. Changes in the level of histone acetylation affect packaging d
NCBI GEO2026 · RNA sequencing · 10 samples
An advanced head-to-tail mouse embryo model with hypoxia-mediated neural patterningThe developing mammalian embryo is guided by the continuously changing signals that it receives from maternal tissues and its microenvironment. The dynamic cell-cell and cell-environment interactions that together shape the embryo largely remained unexplorable until the advance of stem cell-based embryo models. These revealed the self-organizing properties of cells in response to endogenous and ex
NCBI GEO2026 · Excel spreadsheet · 19 samples
Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers [III]Although mutations in genes encoding histones display a similar prevalence to that of some other somatic mutations in cancer, the underlying mechanisms by which histone mutations drive tumorigenesis have not been fully explored. Herein, we curated missense mutations occurring in core histone genes in breast cancers using data from MSK-IMPACT and cBioPortal to identify high frequency breast cancer-
NCBI GEO2026 · RNA sequencing · 22 samples
RNA-binding protein NOC4L governs early natural killer cell development through dual post-transcriptional mechanismsNOC4L is an RNA-binding protein required for early natural killer (NK) cell development. This submission contains: (1) RNA-seq of Noc4l conditional knockout and wild-type NK cells sorted from mouse spleen; (2) two batches of RIP-seq (anti-NOC4L antibody IP with no-antibody and input controls; FLAG-tagged NOC4L IP) identifying NOC4L-bound transcripts in NK cells. Conditional knockout was driven by
NCBI GEO2026 · RNA sequencing · 10 samples
The tRNA Methyltransferase ALKBH8 Promotes Acute Myeloid Leukemia Progression by Regulating Codon-Dependent Gene ExpressionDysregulated mRNA translation is a critical driver of acute myeloid leukemia (AML) progression. Although translation initiation has been extensively studied, the mechanisms governing translation elongation during AML progression remain to be elucidated. Here, we show that the RNA methyltransferase ALKBH8 is overexpressed in AML and is associated with poor prognosis. ALKBH8 is required for the prol
NCBI GEO2026 · Sequencing data · 1 samples
Design and Assembly of Combinatorial DNA Barcodes for Probe-based Genomics Applications [Pyxa spatial transcriptomic]Probe-based genomics technologies are extending molecular analysis into intact tissues and fixed cells, yet strategies to decode complex experimental conditions encoded in cellular RNA remain limited. Here we present a modular framework that integrates custom software tools with purposebuilt cloning reagents to design, assemble, validate, and deploy "combinatorial" DNA barcodes. 25 Combinatorial b
NCBI GEO2026 · Text · 12 samples
icSHAPE profiling of Ebola virus RNA secondary structures in Huh7.5.1 and Vero E6 cellsGenome-wide icSHAPE profiling was performed to determine the secondary structures of Ebola virus RNA in intracellular and extracellular environments, in Huh7.5.1 human hepatocyte-derived cells and Vero E6 monkey kidney cells, defining the structural landscape of the viral genome. By integrating RNA structural data with covariation analysis, evolutionarily conserved RNA structural elements with pot
NCBI GEO2026 · Table · CSV · 145 samples
Spatial Analysis of Placentae During Congenital Cytomegalovirus Infection Suggests Distinct Cellular Profiles in Immune and Trophoblast Cells: An Exploratory StudyHuman cytomegalovirus (CMV) is the leading infectious cause of congenital birth defects worldwide. In this exploratory study, we used the NanoString GeoMx Digital Spatial Profiler to spatially characterize changes in gene expression in CMV+ and control placentae. Given the limited sample size, these findings are descriptive and hypothesis-generating but provide preliminary insight into CMV-associa
NCBI GEO2026 · Text · 61 samples
Genuine-seq enables genome-wide unbiased identification of off-target cleavage and translocation by CRISPR nucleasesCRISPR-Cas system is one of the most widely used tool kit for genome editing. In practice, CRISPR’s causes chromosomal structural variation due to off-targets, which is a serious genotoxicity, while currently unbiased methods for detecting chromosomal structural variation are largely lacking. Here, we developed Genome-wide ubiased identification of nuclease effects by sequencing (Genuine-Seq), whi
NCBI GEO2026 · Text · 8 samples
Genuine-seq enables genome-wide unbiased identification of off-target cleavage and translocation by CRISPR nucleases, IICRISPR-Cas system is one of the most widely used tool kit for genome editing. In practice, CRISPR’s causes chromosomal structural variation due to off-targets, which is a serious genotoxicity, while currently unbiased methods for detecting chromosomal structural variation are largely lacking. Here, we developed Genome-wide ubiased identification of nuclease effects by sequencing (Genuine-Seq), whi
NCBI GEO2026 · RNA sequencing · 33 samples
Dynamic neuro-immune regulation of psychiatric risk loci in human neuronsThe immune environment influences neurodevelopment and subsequent clinical trajectories for psychiatric outcomes in childhood and adolescence. Yet it remains unclear if the impact of maternal and fetal immune activation varies with distinct polygenic risk profiles. Therefore, here we catalogue genotype and environment (GxE) interactions, contrasting allele-specific regulatory activity between infl
NCBI GEO2026 · RNA sequencing · 16 samples
Elucidating the role of IRF4 in reprogramming the tumor microenvironment in follicular lymphomaDespite a characteristic indolent course, a substantial subset of follicular lymphoma (FL) patients has an early relapse with a poor outcome. Thus far, efforts to identify factors that predict survival have been unsuccessful. However, we and others have demonstrated the prognostic relevance of the tumor microenvironment (TME) in FL and provided initial evidence for the role of specific genetic alt
NCBI GEO2026 · Raster · GeoTIFF · 8 samples
Functional Merlin Depletion Defines a TEAD1-Dependent Tumor Cell State that Promotes Schwannoma Progression: Xenium spatial transcriptomicsBiallelic loss of the tumor suppressor NF2/merlin drives vestibular schwannomas (VS). Intratumoral heterogeneity has been observed in VS at the transcriptional, protein expression, and cellular proliferative potential levels, highlighting the need to elucidate the mechanisms underlying heterogeneity in tumor Schwann cell merlin inactivation and therapeutic resistance. Using integrated single-cell
NCBI GEO2026 · RNA sequencing · 32 samples
Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencingThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Raster · GeoTIFF · 15 samples
A single cell and spatial atlas of preinvasive breast cancerDuctal carcinoma in situ (DCIS) is the most common preinvasive breast cancer, however our knowledge of the DCIS tumor microenvironment (TME) remains limited. We constructed a comprehensive atlas of the TME in estrogen-receptor positive DCIS using fresh samples collected from normal breast tissues, DCIS and invasive breast cancers.