Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells

ABSTRACT: Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells

PROVIDER: PRJNA562718 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13512400.fastq.gz	Fastqsanger.gz
	SRR13512500.fastq.gz	Fastqsanger.gz
	SRR13512401.fastq.gz	Fastqsanger.gz
	SRR13512501.fastq.gz	Fastqsanger.gz
	SRR13512402.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 192

Similar Datasets

Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells

Project description:ChIP-seq is the standard technique to characterize the genome-wide epigenomic modifications, which requires millions of cells as starting material. Although some methods have recently reported to be suitable for epigenomic profiling with a small number of cells, there are still no methods capable of profiling both histone modifications and DNA methylation with extremely low input. Here, we developed a new method by supplementing carrier materials of chemically modified epigenetic markers and dUPT-containing DNA fragments during ChIP procedures. Using this strategy, we generated high-quality epigenomic profiles of both histone modifications (super cChIP-seq) and DNA methylation (super cMeDIP-seq) with as few as 10 cells. Thus, we provide a robust and straightforward universal approach for epigenomic profiling starting with extremely low input.

2024-04-07 | GSE136578 | GEO

TimeSignature: A Universal Method for Robust Detection of Circadian State from Gene Expression

Project description:TimeSignature: A Universal Method for Robust Detection of Circadian State from Gene Expression

| PRJNA454445 | ENA

A rapid and robust method for Mitochondrial DNA profiling

Project description:A rapid and robust method for Mitochondrial DNA profiling

| PRJNA1108319 | ENA

Universal and robust bacterial phosphoproteomics analysis

Project description:In present work, we established a simple and robust protocol for universal bacterial phosphoproteomic analysis underlying the rationale of methanol-based LLE protein extraction and cleanup. Using the SDS lysis as the conventional protocol control, we carefully evaluated the efficiency of protein extraction and contaminants removal in terms of phosphopeptide enrichment, phosphopeptide identification and quantification in Listeria monocytogenes, a gram-positive bacterium. We found out the addition of urea, a chaotropic agent, facilitating the protein denaturation and then the protein-impurity dissociation, largely enhanced the protein extraction and sample purity. We further demonstrated the feasibility of this unified LLE platform for studying both gram-positive and gram-negative phosphoproteomes.

2025-08-04 | PXD055159 | JPOST Repository

ChEC-Seq: a robust method to identify protein-DNA interactions genome-wide

Project description:ChEC-Seq: a robust method to identify protein-DNA interactions genome-wide

| PRJNA552083 | ENA

H9 hES cells vs. universal RNAs

Project description:Comparison of human embryonic stem cell transcriptome with universal RNA pool (10 human cell lines) to reveal hES cell-specific gene expression. Keywords: cell type comparison

2007-06-01 | GSE5423 | GEO

Universal Solid-Phase Protein Preparation (USP3) for bottom-up and top-down proteomics

Project description:Selecting a sample preparation strategy for mass spectrometry-based proteomics is critical to the success of quantitative workflows. Here we present a universal, solid-phase protein preparation (USP3) method which is rapid, robust and scalable, facilitating high-throughput protein sample preparation for bottom-up and top-down mass spectrometry (MS) analysis.

2019-06-05 | PXD011169 | Pride

Quantitative Proteomics Identifies Sytenin-1 as a Universal Biomarker of Exosomes

Project description:Exosomes are extracellular vesicles derived from the endosomal compartment. They contain a multitude of bioactive constituents and mediate intercellular communication in health and disease. The frequently used biomarkers of exosomes are heterogeneous and do not exhibit universal utility across different cell types. To uncover ubiquitous and abundant proteins that can serve as universal biomarkers of exosomes, we employed an unbiased and quantitative proteomic approach based on Super SILAC coupled to high-resolution mass spectrometry (MS). In total 1,243 proteins were consistently quantified in the proteome of exosomes, irrespective of the cellular source or isolation method. Among them, a cohort of 22 proteins were universally enriched, and 15 proteins consistently depleted in the proteome of exosomes when compared to cells. Among the enriched proteins, we found several membrane proteins and GTPases, whereas the cohort of depleted proteins was predominantly composed by nuclear proteins. Our study revealed that Syntenin-1 is the most abundant ubiquitous protein in exosomes from distinct cell sources, thus representing an ideal candidate for universal biomarker of exosomes.

2021-06-10 | PXD020260 | Pride

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Project description:CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

| PRJNA631718 | ENA

Towards a universal sample preparation method for denaturing top-down proteomics of complex proteomes

Project description:A universal and standardized sample preparation method becomes vital for denaturing top-down proteomics (dTDP) to advance the scale and accuracy of proteoform delineation in complex biological systems. It needs to have high protein recovery, minimum bias, good reproducibility, and compatibility with downstream mass spectrometry (MS) analysis. Here we employed a lysis buffer containing sodium dodecyl sulfate (SDS) for extracting proteoforms from cells, and for the first time, compared membrane ultrafiltration (MU), chloroform-methanol precipitation (CMP), and single-spot solid-phase sample preparation using magnetic beads (SP3) for proteoform cleanup for dTDP. The MU method outperformed CMP and SP3 methods, resulting in high and reproducible protein recovery from both E. coli cell (59±3%) and human HepG2 cell (86±5%) samples without a significant bias. Single-shot capillary zone electrophoresis (CZE)-MS/MS analyses of the prepared E. coli and HepG2 cell samples using the MU method identified 821 and 516 proteoforms, respectively. Nearly 30% and 50% of the identified E. coli and HepG2 proteins are membrane proteins. CZE-MS/MS identified 94 histone proteoforms from the HepG2 sample with various post-translational modifications, including acetylation, methylation, and phosphorylation. Our results suggest that combining the SDS-based protein extraction and the MU-based protein cleanup could be a universal sample preparation method for dTDP.

2020-05-22 | PXD018248 | Pride

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