Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ultra-parallel ChIP-seq by barcoding of intact nuclei

ABSTRACT: Ultra-parallel ChIP-seq by barcoding of intact nuclei

PROVIDER: PRJNA435556 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6761490_1.fastq.gz	Fastqsanger.gz
	SRR6761490_2.fastq.gz	Fastqsanger.gz
	SRR6761500_1.fastq.gz	Fastqsanger.gz
	SRR6761500_2.fastq.gz	Fastqsanger.gz
	SRR6761510_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 232

Similar Datasets

Ultra-parallel ChIP-seq by barcoding of intact nuclei

Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples. Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources. Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.

2018-03-06 | GSE111000 | GEO

Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state

Project description:Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow-injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed 6 ubiquitin-barcoded CRISPRi strains targeting metabolic enzymes, and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.

2024-10-30 | MSV000096254 | MassIVE

PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

Project description:PAN-INTACT method can be used to isolate cell type specific nuclei from fibrous mouse organs, which are particularly problematic. It is broadly applicable for profiling the transcriptional and epigenetic landscape of specific cell types. We envision that our method can be used to systematically probe mechanistic details of cell type-specific functions within individual organs of intact mice.

2019-04-05 | GSE119792 | GEO

AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq

Project description:AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq

| PRJNA612844 | ENA

PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

Project description:PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

| PRJNA490328 | ENA

INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison

Project description:In this study we used transgenic mouse model to comapre two isolation techniques INTACT and FANS for the isolation of activated neuronal nuclei. Comparison is perfomed on multiple levels like isolation efficiency, membrane integrity, transcriptional and epigenetic state using RNA-seq and ATAC-seq

2021-01-28 | GSE165644 | GEO

Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei

Project description:Cells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. From this data we constructed an overview of the nuclear interactome. We observed that the histone proteins on the nucleosomes expose well-defined crosslinking hot-spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build models of their binding mode to the nucleosome. For HMGN2 the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS and modeling. Excitingly, several isoform-specific interactors seem to exist for distinct histone H1 variants and the analysis of crosslinks carrying post-translational modifications allowed us to extract how specific modifications influence the nucleosome interactome. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.

2018-07-23 | PXD007513 | Pride

Ultra-High Throughput Single Cell Analysis of Proteins and RNAs by Split-pool Synthesis

Project description:We report a method enabling simultaneous, ultra-high throughput single-cell-barcoding, of millions of cells for targeted single cell analysis of proteins and RNAs. This method termed Quantum Barcoding (QBC) circumvents the need to isolate single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette) cell-specific codes are added to each tagged molecule within cells. This is accomplished through sequential rounds of the well-established process of classic “split-pool synthesis”. We demonstrate the utility of this currently research use only technology in multiple model systems.

2019-05-07 | GSE130784 | GEO

INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison

Project description:INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison

| PRJNA695261 | ENA

CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC]

Project description:We reported a Concanavalin A-based Barcoding Strategy (CASB) for single-cell and single-nucleus sample multiplexing, which could be followed by different single-cell sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. Besides sample multiplexing, the CASB could further improve data quality through doublet identification.

2021-03-09 | GSE153115 | GEO

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