Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

ABSTRACT: SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

OTHER RELATED OMICS DATASETS IN: GSE63266

PROVIDER: PRJNA267121 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1649860.fastq.gz	Fastqsanger.gz
	SRR1649870.fastq.gz	Fastqsanger.gz
	SRR1649880.fastq.gz	Fastqsanger.gz
	SRR1649890.fastq.gz	Fastqsanger.gz
	SRR1649900.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 588

Similar Datasets

SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

Project description:Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. The SC3-seq allows excellent quantitative measurement of mRNAs ranging from the 10,000-cell to 1-cell level, and accordingly, allows an accurate estimate of the transcript levels by a regression of the read counts of spike-in RNAs with defined copy numbers. The SC3-seq has clear advantages over other typical single-cell RNA-seq methodologies for the quantitative measurement of transcript levels and at a sequence depth required for the saturation of transcript detection. The SC3-seq distinguishes four distinct cell types in the peri-implantation mouse blastocysts. Furthermore, the SC3-seq reveals the heterogeneity in human-induced pluripotent stem cells (hiPSCs) cultured under on-feeder as well as feeder-free conditions, demonstrating a more homogeneous property of the feeder-free hiPSCs. We propose that SC3-seq might be used as a powerful strategy for single-cell transcriptome analysis in a broad range of investigations in biomedical sciences.

2015-03-20 | GSE63266 | GEO

MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

Project description:Abstract: Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Finally, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics simulation energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for pre-screening interactions, but that measuring interactions experimentally remains necessary to rank their strengths quantitatively.

2024-07-12 | GSE271790 | GEO

SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

| S-EPMC4482058 | biostudies-literature

MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

Project description:MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

| PRJNA1133167 | ENA

Massively Parallel Binding Assay (MPBA) reveals limited transcription factor cooperation, challenging models of specificity

Project description:We provide the data collected using the method MPBA, allowing parallel measurement of TF binding to thousands of DNA sequence-variants within cells. The method was applied to quantify binding of dozens of transcription factors (TFs) to libraries of mutated regulatory regions, systematically screening all motif combinations.

2024-06-26 | GSE234455 | GEO

Highly parallel quantification and compartment localization of transcription factors and nuclear proteins

Project description:Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly-parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables systems-level study of previously inaccessible chromatin and genome regulators.

2020-02-17 | GSE140325 | GEO

Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (VI)

Project description:Anti-oxidation metabolism measurement in mouse CSF by quantitative LC/MS method.

2021-09-15 | ST001979 | MetabolomicsWorkbench

Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (V)

Project description:Anti-oxidation metabolism measurement in human patient CSF by quantitative LC/MS method.

2021-09-15 | ST001978 | MetabolomicsWorkbench

Anti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (IV)

Project description:Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method of human patient/lymphoma patient CSF.

2021-09-15 | ST001977 | MetabolomicsWorkbench

Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (III)

Project description:Anti-oxidative metabolism measurement in mouse CSF by quantitative LC/MS method of mouse CSF at 24H of MTX treatment, for either control GFP or SOD3-overexpressing ChP mice.

2021-09-14 | ST001976 | MetabolomicsWorkbench

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