Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]

ABSTRACT: We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.

ORGANISM(S): Homo sapiens

PROVIDER: GSE105452 | GEO | 2019/02/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]

Project description:Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]

| PRJNA415205 | ENA

Assembly of full-length macaque gene models

Project description:We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

2021-06-01 | GSE132413 | GEO

Full-length mRNA sequencing reveals principles of poly(A) tail length control

Project description:We report FLAM-seq, a cDNA library preparation method coupled to PacBio single-molecule sequencing for profiling full-length mRNAs including their poly(A) tail.

2019-06-04 | GSE126465 | GEO

Full-length sequencing of HLA genes

Project description:Single molecule real-time (SMRT) DNA sequencing of HLA genes

| PRJEB22131 | ENA

Benchmarking full-length transcript single cell mRNA sequencing protocols

Project description:Here we present a performance evaluation of three different plate-based scRNA-seq protocols. Two commercially available kits; NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T). We evaluated each kit based upon sensitivity, reproducibility, ease of use and price point per cell. This evaluation is specifically relevant for implementation of scRNA-seq in e.g. diagnostics, requiring high sensitivity in regards of gene detection, high reproducibility between samples, minimum hands on time and smooth sample preparation for technicians, as well as keeping a reasonable price point per patient. G&T protocol delivered the highest detection of genes per single cell, at the absolute lowest price point. Takara's kit delivered likewise high gene detection per single cell, and high reproducibility between sample, however at the absolute highest price points. Here we present pros and cons of each protocol, sequencing breast cancer cell line T47D.

2020-08-01 | GSE155506 | GEO

Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells

Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells.

2013-09-01 | GSE49321 | GEO

Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells

Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells. Cells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2).

2013-09-01 | E-GEOD-49321 | biostudies-arrayexpress

Rescue of murine Gata1s mutant M7 leukemic cells by full-length Gata1

2010-08-01 | GSE16676 | GEO

Rescue of murine Gata1s mutant M7 leukemic cells by full-length Gata1

Project description:In this project, we studied a mouse model of human Down Syndrome (DS) megakaryocytic leukemia involving mutations in the GATA1 transcription factor (called GATA1s mutation). The model was generated through retroviral insertional mutagenesis in Gata1s mutant fetal liver progenitors. In this study, we analyzed the dependency of these leukemic cells on the Gata1s mutant protein. Here we report Gata1s mutant leukemic cells were dependent on this mutant protein. Introduction of the full-length Gata1 protein to these cells led to their reduced proliferation and increased differentiation along the megakaryocytic lineage. We transduced leukemic cells with Gata1/estrogen receptor fusion cDNA (Gata1-ER) and generated stable cell lines. Addition of beta-estradiol to culture medium led to activation of the full-length Gata1 protein in synchronized leukemic cells. Gene expression profiles were collected at multiple time points.

2010-08-01 | E-GEOD-16676 | biostudies-arrayexpress

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms

Project description:Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we established an experimental and computational pipeline that accurately quantifies transcript isoforms in their entire length from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generated a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms (http://steinmetzlab.embl.de/iBrowser/). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identified 121 differentially expressed transcript isoforms in 107 cardiac genes. By establishing an isoform-differential expression test, our approach revealed that 11 of these genes displayed no detectable change in overall RNA expression. However, significant differences in the expression of specific isoforms in these genes was observed. These isoform specific effects demonstrate the need of analyzing RNA isoform expression levels rather than total gene expression levels.

2021-06-16 | E-MTAB-7334 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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