Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE140325 | GEO | 2020/02/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description:Highly parallel quantification and compartment localization of transcription factors and nuclear proteins

| PRJNA589292 | ENA

Massively parallel quantification of the regulatory effects of non-coding genetic variation [STARR-seq]

Project description:We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter-gene expression assay. As demonstration, we have measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. We found that, in agreement with previous reports, most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify likely causal regulatory haplotypes that contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses. 104 candidate regulatory elements from 95 individuals were resequenced using Illumina custom amplicon sequencing. We then cloned the resulting DNA fragments into a massively parallel reporter assay to quantify allele-specific regulatory activity from that population. SNP-fdr.txt contains output of significance evaluation haplotype.fasta.gz contains the reference used to generate alignment files

2015-06-15 | E-GEOD-68331 | biostudies-arrayexpress

Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA

Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA.

2015-03-04 | GSE66478 | GEO

Chromatin-enriched RNA sequencing of HL-1 mouse cardiomyocytes

Project description:Biochemical fractionation of HL-1 mouse cardiomyocyte nuclei and RNA-seq of chromatin-enriched and soluble-nuclear RNA

2023-12-31 | GSE164126 | GEO

Massively parallel quantification of the regulatory effects of non-coding genetic variation

2015-06-15 | GSE68331 | GEO

Quantification of subcellular mRNA kinetics in mouse embryonic stem cells

Project description:In this work, we quantified mRNA flow rates between subcellular compartments in mouse embryonic stem cells. Combining metabolic RNA labeling, biochemical cell fractionation and RNA sequencing with mathematical modeling we were able to determine the kinetic rates of nuclear pre-, nuclear mature, cytosolic and membrane mRNA derived from more than 9000 protein-coding genes. For more than 5000 genes, we additionally estimated the transcript elongation rate. For most of the transcripts, mature nuclear half-lives are the longest, suggesting nuclear retention to be the rate-limiting step in the mRNA life cycle. Genes encoding transcription factors and immediate early genes possess fast kinetic rates, specifically a short nuclear half-life. Differentially localized mRNAs exhibit distinct combinations of rate constants, suggesting modular control within subcellular compartments. We show that membrane stability is high for membrane-localized mRNA and that cytosolic stability is high for cytosol-localized mRNA. Genes encoding target signals, such as signal peptides or transmembrane domains, have low cytosolic and high membrane half-lives with only slight differences between target signals. Nuclear-encoded mitochondrial proteins show long nuclear mature half-lives and otherwise similar features of cytoplasmic kinetics that do not resemble co-translational targeting to the mitochondria.

2024-09-17 | GSE252199 | GEO

CscoreTool-M infers 3D sub-compartment probabilities within cell population

Project description:Motivation: Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data. Results: The compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions. Availability: https://github.com/scoutzxb/CscoreTool-M

2023-05-31 | GSE224282 | GEO

Quantification of acetylation stoichiometry in SLC13A5/NaCT and SLC25A1/CIC neuron-specific overexpression (nTg) models in mouse cortex and hippocampus

Project description:Acetylation stoichiometry quantification in SLC13A5/NaCT and SLC25A1/CIC neuron specific over expression (nTg) mouse model compared to wildtype controls. Subcellular fractionation of cortex and hippocampus into cytoplasmic/mitochondrial (CyMi), nuclear (ChEx), and chromatin associated (450).

2021-04-15 | MSV000087209 | MassIVE

Quantification of subcellular mRNA kinetics in mouse embryonic stem cells (flavopiridol)

2024-09-17 | GSE256335 | GEO

Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA

Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA. Nuclei from three biological replicates were isolated by detergent lysis, fractionated, then three chromatin and three soluble RNA samples were converted to cDNA using Illumina TruSeq stranded protocol, and sequenced on Illumina HiSeq2000

2015-03-04 | E-GEOD-66478 | biostudies-arrayexpress

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