Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing III

ABSTRACT: Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

ORGANISM(S): Mus musculus

PROVIDER: GSE266160 | GEO | 2024/05/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing II

Project description:Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

2024-05-07 | GSE266117 | GEO

RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I

2024-05-07 | GSE265962 | GEO

RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-05-07 | GSE266161 | GEO

Transcriptome sequencing of the rock pigeon, Columba livia

Project description:Deep sequencing of mRNA from the rock pigeon Analysis of ploy(A)+ RNA of different specimens: heart and liver from the rock pigeon (Danish Tumbler, Oriental Frill and Racing)

2013-02-03 | E-GEOD-39333 | biostudies-arrayexpress

Transcriptome sequencing of the rock pigeon, Columba livia

Project description:Deep sequencing of mRNA from the rock pigeon

2013-02-03 | GSE39333 | GEO

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of TFs from a single experiment

Project description:Detecting differential activation of transcription factors (TFs) in response to perturbation provides insight into global cellular processes. We present here Transcription Factor Enrichment Analysis (TFEA), a robust and reliable computational method that can detect differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional motif enrichment within an ordered list of regions of interest (ROI). As ROI are typically directly inferred from the data, we also introduce muMerge, a statistically principled method that generates a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data types that inform on transcriptional regulation, including CAGE data, ChIP-Seq, and accessibility data (e.g. ATAC-Seq). We demonstrate that TFEA can not only identify key TFs that respond to a perturbation, but also temporally unravel complex regulatory networks with time series data. Consequently, TFEA serves as a “hypothesis-generating engine” that provides an easy, rigorous, and cost-effective means to broadly assess TF activity to yield new biological insights about basic cellular processes.

2020-12-18 | GSE142419 | GEO

Pyrosequencing Analysis of Microbial Communities in Rock Varnish

Project description:This study investigated the microbial community of rock varnish Based on consensus sequences for 16S OTUs

2013-04-26 | E-GEOD-46347 | biostudies-arrayexpress

Pyrosequencing Analysis of Microbial Communities in Rock Varnish

Project description:This study investigated the microbial community of rock varnish

2013-04-26 | GSE46347 | GEO

Reduced expression of RhoE promotes ROCK-dependent invasion in transformed human fibroblasts

Project description:Cen3tel cells, obtained by telomerase immortalization of human fibroblasts, gradually underwent neoplastic transformation and became metastatic in immunocompromised mice. Neoplastic transformation was associated with a change in cell morphology (from fibroblastic to polygonal). Tumorigenic cells acquired a clear-cut membrane localization of adhesion molecules, a reorganization of the actin cytoskeleton, increased cell motility and invasiveness. In a 3-dimensional environment, tumorigenic cells showed a spherical morphology with cortical actin rings, suggesting a switch from a mesenchymal to an amoeboid ROCK-dependent movement. Accordingly, cell invasion decreased upon treatment with the ROCK inhibitor Y27632, but not with the matrix protease inhibitor Ro28-2653. The increased invasiveness of tumorigenic cen3tel cells was associated with a reduced expression of RhoE, a cellular inhibitor of ROCK. Ectopic RhoE expression decreased cen3tel invasion capability. These results point to RhoE and ROCK as regulators of invasiveness of mesenchymal tumor cells and indicate ROCK as a possible therapeutic target. The cen3tel telomerase immortalized cell line was obtained from primary cen3 fibroblasts, derived from a centenarian individual, by infection with an hTERT-containing retrovirus (Mondello et al., 2003). Cen3tel cells were used at different steps of propagation, reflecting different phases of transformation (Zongaro et al., 2005) to study variations in the migratory and invasive potential accompanying human fibroblast neoplastic transformation. Raw data files: *NORM.txt test is Cy5 and *DS.txt test is Cy3.

2011-04-20 | E-GEOD-15742 | biostudies-arrayexpress

Reduced expression of RhoE promotes ROCK-dependent invasion in transformed human fibroblasts

2011-04-20 | GSE15742 | GEO

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