Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Case Report: Multimodal optical imaging and genetic features of AB variant GM2 gangliosidosis

PROVIDER: PRJNA962274 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24320201_1.fastq.gz	Fastqsanger.gz
	SRR24320201_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Project description:Case report: Novel genetic variant associated with epilepsy

| PRJNA956710 | ENA

Project description:Case Report: Clinical and Genetic features in a case of pediatric choroidal melanoma

| PRJEB85793 | ENA

Project description:New Clinical Features and a Novel DCDC2 Variant in Neonatal Sclerosing Cholangitis: A Case Report of Two Patients

| PRJNA1251848 | ENA

Integrating single-cell RNA-seq and imaging with SCOPE-seq2

Project description:Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from the transcriptome. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2), which builds on our earlier efforts to combine single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrated the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.

2020-06-28 | GSE151137 | GEO

Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics

Project description:Spatially targeted optical microproteomics (STOMP) is a novel proteomics technique for interrogating micron-scale regions of interest (ROI) in mammalian tissue, with no requirement for genetic manipulation. Methanol or formalin fixed specimens are stained with fluorescent dyes or antibodies to visualize ROIs, then soaked in solutions containing the photo-tag: 4-benzoylbenzyl-glycyl-hexahistidine. Confocal imaging along with two photon excitation are used to covalently couple photo-tags to all proteins within each ROI, to a resolution of 0.67 µm in the xy-plane and 1.48 µm axially. After tissue solubilization, photo-tagged proteins are isolated and identified by mass spectrometry. As a test case, we examined amyloid plaques in an Alzheimer’s disease (AD) mouse model and a postmortem AD case, confirming known plaque constituents and discovering new ones. STOMP can be applied to various biological samples including cell lines, primary cell cultures, ex vivo specimens, biopsy samples and fixed postmortem tissue.

2015-11-18 | PXD002959 | Pride

Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

Project description:Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

2021-06-03 | GSE158732 | GEO

Case Report: Molecular Profiling Facilitates the Diagnosis of a Challenging Case of Lung Cancer with Choriocarcinoma Features

Project description:Case Report: Molecular Profiling Facilitates the Diagnosis of a Challenging Case of Lung Cancer with Choriocarcinoma Features

| PRJNA1087426 | ENA

Project description:Innovative Diagnostic Approaches and Multimodal Therapy: A Case Report of Severe Pediatric Scrub Typhus with Complications

| PRJNA1157000 | ENA

E-MTAB-1356

Project description:Transcription profiling by array of H. sapiens acute myeloid leukemia mononuclear cells to investigate associations with distinct clinical and genetic features and lack KIT mutations

2025-01-23 | E-MTAB-1356 | ExpressionAtlas

Transcription profiling of human primary liver tumours vs. universal human reference reveals that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer

Project description:Segal et al., 2007, Nature Biotechnology (doi:10.1038/nbt1306): Decoding global gene expression programs in liver cancer by noninvasive imaging. ABSTRACT: Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. Here we show that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer. Combinations of twenty-eight imaging traits can reconstruct 78% of the global gene expression profiles, revealing cell proliferation, liver synthetic function, and patient prognosis. Thus, genomic activity of human liver cancers can be decoded by noninvasive imaging, thereby enabling noninvasive, serial and frequent molecular profiling for personalized medicine.

2007-06-06 | E-SMDB-3992 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data