Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.

ABSTRACT: Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE31602 | GEO | 2011/12/05

SECONDARY ACCESSION(S): PRJNA145583

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.

Project description:Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle. We determined genes preferentially expressed in muscle cells of adult C. elegans by analyzing RNA from total and affinity-puridied muscle nuclei using microarrays. We also determined the nucleosome occupancy in these nuclei by micrococcal nuclease mapping and paired-end sequencing.

2011-12-05 | E-GEOD-31602 | biostudies-arrayexpress

INTACT method for gene expression and chromatin profiling of individual cell types within a tissue

2010-06-14 | GSE19654 | GEO

Protocol for the purification and transcriptomic analysis of mouse astrocytes using GFAT

Project description:Astrocytes are glial cells of the central nervous system that modulate neuronal function. Here, we present glyoxal-fixed astrocyte nuclei transcriptomics (GFAT), a protocol for the purification and transcriptomic analysis of astrocyte nuclei from the cortex and cerebellum of adult and aged fresh mouse brain. We describe steps for tissue dissection, glyoxal fixation, homogenization, nuclei isolation, antibody staining, fluorescence-activated cell sorting, and RT-qPCR or bulk RNA sequencing. GFAT does not require transgenic lines or viral injection and allows parallel astrocyte and neuron profiling.

2023-09-15 | GSE233509 | GEO

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 method for gene expression and chromatin profiling of individual cell types within a tissue

Project description:We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. Keywords: Chromatin affinity-purification on microarray All experiments were done using two channels per chip. Two types of experiments were performed. Expression profiling was performed by comparing cDNAs synthesized from nuclear RNA isolated from INTACT-prepared Arabidopsis nuclei to total sonicated genomic DNA isolated from Arabidopsis plants. Chromatin profiling was performed using INTACT-prepared Arabidopsis nuclei. DNA isolated by Chromatin immunoprecipitation (ChIP) using antibodies to modified histones was compared to histone H3 ChIP DNA from the same sample.

2010-06-13 | E-GEOD-19654 | biostudies-arrayexpress

Genome-wide analysis of gene expression in proliferative dentate gyrus (DG) nuclei of adult wild-type and KMT2D-deficient mice

Project description:We conducted genome wide transcription profiling by RNA-seq in proliferating neuronal progenitors after purifying EdU+ nuclei from micro-dissected DG of adult wild-type and KMT2D-deficient mice (Kmt2d +/Bgeo)

2019-02-07 | GSE126164 | GEO

mini-INTACT reveals social isolation-induced epigenetic changes in Drosophila dopaminergic neurons

Project description:We introduce a more sensitive method for purifying specific cell-types from small numbers of fly heads for epigenomic analysis: a method we call ‘mini-INTACT’. We modified the INTACT method in Drosophila [Henry G. L. et al., Nucleic Acids Research, 2012, 1–14] to enable purification of genetically tagged rare cell types from Drosophila brain requiring ~50-100 fold less material. We used male fruit flies as a model to examine the effects of social-isolation vs. social-enrichment on the epigenome and transcriptome of dopaminergic neurons defined by expression of the TH-GAL4 driver. Using ChIP-seq on mini-INTACT purified nuclei, RNA-seq and bioinformatic analysis, we identify regulation of the transcriptome and behavior by Activity Related Genes who’s expression is induced by social enrichment.

2019-02-07 | GSE126186 | GEO

Cell type purification by single-cell transcriptome-trained sorting

Project description:Traditional cell type enrichment using fluorescence activated cell sorting (FACS) relies on methods that specifically label the cell type of interest. Here we propose GateID, a computational method that combines single-cell transcriptomics, for unbiased cell type identification, with FACS index sorting, to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without resorting to specific antibodies or transgenes.

2019-10-07 | GSE112438 | GEO

Efficient detection and purification of cell populations using synthetic microRNA switches

Project description:Isolation of specific cell types, including pluripotent stem cell (PSC)-derived populations, is frequently accomplished using cell surface antigens expressed by the cells of interest. However, specific antigens for many cell types have not been identified, making their isolation difficult. Here, we describe an efficient method for purifying cells based on endogenous miRNA activity. We designed synthetic mRNAs encoding a fluorescent protein tagged with sequences targeted by miRNAs expressed by the cells of interest. These miRNA switches control their own translation levels by sensing miRNA activities. Several miRNA switches (miR-1-, miR-208a-, and miR-499a-5p-switches) efficiently purified cardiomyocytes differentiated from human PSCs, and switches encoding the apoptosis inducer Bim enriched for cardiomyocytes without cell sorting. This approach is generally applicable, as miR-126-, miR-122-5p- and miR-375-switches purified endothelial cells, hepatocytes and INSULIN-producing cells differentiated from hPSCs, respectively. Thus, miRNA switches can purify cell populations for which other isolation strategies are unavailable.

2015-05-20 | GSE60633 | GEO

Nuclear and cellular mRNA sequencing of 1 cm root tips of 7 days Oryza sativa seedlings

Project description:Plants dynamically regulate chromatin architecture, transcription and post-transcriptional processes in accordance with developmental programs and environmental cues. Isolated nuclei can provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain with an outer nuclear envelope-anchored domain in the Nuclear Tagging Fusion protein and codon optimization of E. coli BirA, combined in a single T-DNA construct. We also developed an inexpensive methods for INTACT, T-DNA insertion mapping, and profiling of the complete nuclear transcriptome, including a rRNA degradation procedure that minimizes pre-rRNA transcripts. The comparison of nuclear and steady-state poly(A)+ transcript populations of seedling root tips confirmed the capture of pre-mRNA and exposed distinctions between the nuclear and total RNA pool. The improved INTACT plasmid configuration for monocots and accompanying methods provide access to chromatin and pre-mRNA, paving the way for monitoring nuclear transcriptome and epigenome dynamics of specific cell-types in rice and other crop species.

2017-09-19 | GSE99122 | 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