Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Joint representation and visualization of derailed cell states with Decipher

ABSTRACT: Joint representation and visualization of derailed cell states with Decipher

PROVIDER: PRJNA1271999 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33834300_1.fastq.gz	Fastqsanger.gz
	SRR33834300_2.fastq.gz	Fastqsanger.gz
	SRR33834301_1.fastq.gz	Fastqsanger.gz
	SRR33834301_2.fastq.gz	Fastqsanger.gz
	SRR33834302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 289

Similar Datasets

Joint representation and visualization of derailed cell states with Decipher [scATAC-seq]

Project description:Joint representation and visualization of derailed cell states with Decipher [scATAC-seq]

| PRJNA1272091 | ENA

Joint representation and visualization of derailed cell states with Decipher

Project description:Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.

2025-06-04 | GSE298955 | GEO

Joint representation and visualization of derailed cell states with Decipher [scATAC-seq]

2025-06-05 | GSE299002 | GEO

Joint representation and visualization of derailed cell states with Decipher.

Project description: Not available

| S-EPMC10680623 | biostudies-literature

Joint representation and visualization of derailed cell states with Decipher

Project description: Not available

| S-EPMC12285193 | biostudies-literature

GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)

Project description:Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This submission contains the Cell Ranger ARC processed outputs from single nuclei joint transcriptome- and chromatin accessibility-sequencing (10x Genomics). We also provide an integrated single nuclei transcriptomics dataset, comprised of malignant and tumour microenvironment cell type annotations.

2026-06-12 | E-MTAB-17183 | biostudies-arrayexpress

VPBrowse, genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins

Project description:SWATH is a mass spectrometry data acquisition strategy that relies on peptide spectral libraries to perform quantitatively accurate and consistent measurement of proteins across multiple samples. Public libraries have been developed for humans and several laboratory species that have accelerated biomarker discovery, and similarly comprehensive resources would be useful for other species. The Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), is an on-line platform developed for genome-based representation of the Bos taurus proteome and is equipped with an interactive database and tools for visualization and building quantitative mass spectrometry assays. VPBrowse contains high quality tandem mass spectrometry (MS/MS) spectra acquired on QToF instrument for over 36,000 proteotypic peptides corresponding to over 10,000 bovine proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to 25 different tissues and body fluids, the resource supported label-free quantification of nearly 30% of the protein-coding genes annotated in bovine section of UniprotKB.

2024-03-07 | PXD044768 | Pride

miRNAs expression in joint of Collagen-induced arthritis (CIA)

Project description:MicroRNAs (miRNAs) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases. By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases, as well as their relevant mouse models such as CIA. We isolated joint samples pooled from six CIA mice or from six naM-CM-/ve control mice. Total RNA was extracted for the TaqManM-BM-. Low Density Assay v3.0

2012-12-19 | E-GEOD-37422 | biostudies-arrayexpress

mNGS bone joint

Project description:mNGS bone joint

| PRJEB72431 | ENA

Visualization of individual cell division history in complex tissues

Project description:Visualization of individual cell division history in complex tissues

| PRJNA704410 | ENA