Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inferring regulatory targets of transcription factors from simultaneous single cell measurements of intranuclear proteins and gene expression

ABSTRACT: Simultaneous single cell measurements of nuclear proteins and RNA with inCITE-seq, with targeted protein measurements using DNA-conjugated antibodies. Single nuclei (n=10,014) of HeLa cells, either untreated or after TNFa treatment, were profiled with inCITE-seq targeting the transcription factor p65. Single nuclei (n=21,583) of the mouse hippocampus after PBS or kainic acid injection were profiled with inCITE-seq targeting TFs p65, c-Fos, and PU.1, as well as the RNA-binding protein NeuN.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE163480 | GEO | 2021/07/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single nucleus RNAseq of cerebellar nucleus neurons in three species

Project description:We perform single nucleus RNAsequencing using a smartseq2 protocol on mouse, chicken, and human cerbellar nuclei. Nuclei were released and FACS sorted for NeuN

2020-10-30 | GSE160471 | GEO

Human cortical nuclei RNAseq

Project description:RNA-seq of NeuN-negative and NeuN-positive nuclei from healthy controls

2021-02-28 | GSE150121 | GEO

Inferring regulatory targets of transcription factors from simultaneous single cell measurements of intranuclear proteins and gene expression

Project description:Inferring regulatory targets of transcription factors from simultaneous single cell measurements of intranuclear proteins and gene expression

| PRJNA686382 | ENA

Brain neuronal cell nuclei with exceptionally high levels of hydroxymethylcytosine

Project description:We recently reported that a significant subpopulation of adult mouse brain cellular nuclei (NeuN-High) have highly decondensed chromatin characteristic of multipotent cells types (Yu et al., DNEU, 2015). Herein we show that NeuN-High nuclei also have significantly higher levels of 5´-hydroxymethylcytosine (5hmC), a rate limiting intermediate in the turnover of modified cytosine. TET-assisted bisulfite sequencing demonstrated that 5hmC levels in NeuN-High nuclei spiked rapidly from 20% to nearly 40% of CG dinucleotides at the start of gene regions for various classes of the most highly transcribed neuron-specific genes, but were variably distributed among different functional gene categories and in well-defined gene regions. NeuN-Low neuronal and non-nueronal neuronal nuclei had significantly lower levels of 5hmC for all classes of expressed genes. In summary, these data support the view that an elevated turnover rate for chromatin modifications may potentiate the cellular memory of the most active subclasses of neurons.

2022-07-07 | GSE72432 | GEO

CdLS NeuN-positive RNAseq

Project description:RNA-seq of NeuN-positive nuclei from CdLS patients and healthy age-matched controls

2021-02-28 | GSE150118 | GEO

CdLS NeuN-negative RNAseq

Project description:RNA-seq of NeuN-negative nuclei from CdLS patients and healthy age-matched controls

2021-02-28 | GSE150117 | GEO

CdLS NeuN-positive ATACseq

Project description:ATAC-seq of NeuN-positive nuclei from CdLS patients and healthy age-matched controls

2021-02-28 | GSE150079 | GEO

Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain [ChIP-Seq]

Project description:Trimethylated histone H3-lysine 4 is primarily distributed in the form of sharp peaks, extending in neuronal chromatin on average only across 500-1500 base pairs mostly in close proximity to annotated transcription start sites. To explore whether H3K4me3 peaks could also extend across much broader domains, we undertook a detailed analysis of broadest domain cell-type specific H3K4me3 peaks in ChIP-seq datasets from sorted neuronal and non-neuronal nuclei in human, non-human primate and mouse prefrontal cortex (PFC), and blood for comparison. In this GEO submission, we list six newly generated ChIP-seq data sets. FACS sorted Neuronal (NeuN+) nuclei and non-neuronal (NeuN-) nuclei collected from prefrontal cortex (PFC) and processed by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). In addition we collected nucleated blood cells from 3 control subjects. These are additional subjects unrelated to brain cohort.

2016-07-21 | E-GEOD-72929 | biostudies-arrayexpress

Nuclear proteome of cortical neurons of young and aged mice

Project description:Mass spectrometry analysis of NeuN-positive neuronal nuclei from cortices of young and aged mice

2023-07-21 | PXD041560 | JPOST Repository

The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

Project description:This submission is a dataset of two modalities, single-nucleus transcriptomics and single-nuclei spatial transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using 10x Genomics Chromium Single Cell Kit Version. The single-nuclei spatial transcriptomics data is harvested and profiled using Visium Spatial Gene Expression.

2024-01-30 | GSE234774 | 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