Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SnRNA Visium Spatial data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs 23 months

ABSTRACT: Using 23-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000. Processed count matrices, metadata and objects with filtered, clustered, and annotated data can be found on Zenodo: 10.5281/zenodo.14988055

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mouse

SUBMITTER: Jaehyun Lee

PROVIDER: E-MTAB-15158 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

snRNA data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs

Project description:Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000.

2025-03-15 | E-MTAB-14889 | biostudies-arrayexpress

snRNA-seq for Macaque LIP

Project description:snRNA-sequencing data for macaque LIP area. We isolated single nuclei from the LIP region. annotating the dataset with the canonical classification and integration with other datasets.

2026-05-31 | E-MTAB-13364 | biostudies-arrayexpress

A gene regulatory network for neural induction

Project description:During early vertebrate development, signals from a special region of the embryo, the organizer, can re-direct the fate of non-neural ectoderm cells to form a complete, patterned nervous system. This is called neural induction and has generally been imagined as a single signaling event, causing a switch of fate. Here we undertake a comprehensive analysis, in very fine time-course, of the events following exposure of ectoderm to the organizer. Using transcriptomics and epigenomics we generate a Gene Regulatory Network comprising 175 transcriptional regulators and 5,614 predicted interactions between them, with fine temporal dynamics from initial exposure to the signals to expression of mature neural plate markers. Using in situ hybridization, single-cell RNA-sequencing and reporter assays we show that neural induction by a grafted organizer mimics normal neural plate development. The study is accompanied by a comprehensive resource including information about conservation of the predicted enhancers in different vertebrate systems.

2023-03-13 | E-MTAB-10426 | biostudies-arrayexpress

Single-cell RNAseq of mouse brain infected with Langat virus in WT and Ifnar KO

Project description:In this project we studied the effect of Langat infection (LGTV strain TP21) on the brains of mice, both wild-type and Ifnar-/-. Nuclei of the brain were isolated and subjected to 10x 3' scRNAseq.

2023-03-19 | E-MTAB-12131 | biostudies-arrayexpress

Chromatin accessibility in human monocytes differentiation (3D-MO)

Project description:This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.

2022-06-24 | E-MTAB-10846 | biostudies-arrayexpress

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

Project description:5-Hydroxymethylcytosine (hmC) is particularly abundant in mammalian brains with yetto be revealed functions. Here, we present genome-wide and single-base-resolutionmaps of hmC and mC in the human brain. We demonstrated that hmCs increasemarkedly from the fetal to the adult stage, and in the adult brain, 13.4% of all CpGs arehighly hydroxymethylated with strong enrichment at genic regions and distal regulatoryelements. Notably, hmC peaks were identified at the 5' splicing sites at the exon-intronboundary, suggesting a mechanistic link between hmC and splicing. We also report asurprising transcription-correlated hmC bias toward the sense strand and an mC biastoward the antisense strand of gene bodies. Furthermore, hmC is negatively correlatedwith H3K27me3-marked repressive genomic regions, and is more enriched in poisedenhancers than active enhancers. Our results provide insights into understanding themultiple potential functions of hmC in the human brain. A cell type specific hydroxymethylome sample of NeuN+ neurons in frontal lobe from the same adult individual, whose TAB-Seq data was deposited in GSE46710

2014-02-22 | E-GEOD-55249 | biostudies-arrayexpress

Nuclear RNA immunoprecipitation of MEN1 in MCF-7 BC cell line

Project description:To understand molecules involved in DOT1L-menin-ERα complex formation, we performed a native nuclear RIP-Seq approach in MCF-7 BC cell line. Here, we submit 3 samples immunoprecipitated with anti-MEN1 and two samples with anti-IgG (E-MTAB-14147).

2026-01-30 | E-MTAB-15354 | biostudies-arrayexpress

Nuclear RNA immunoprecipitation of ERα in MCF-7 BC cell line

Project description:Native nuclear RNA immunoprecipiatation of the estrogen receptor α (ERα) in exponentially growing MCF-7 for the identification of RNAs linked to the receptor.

2025-02-14 | E-MTAB-14147 | biostudies-arrayexpress

SF3B1 association with chromatin determines splicing outcomes

Project description:Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. Part of the explanation probably lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicated that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses revealed that SF3B1 is specifically bound to nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC content between exons and introns. Disruption of SF3B1 binding to such nucleosomes affected the splicing of these exons similarly to inhibition of SF3B1 expression. Our findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure. MNase-seq on Input and SF3B1 pull-down, mRNA-seq on control and SF3B1 si-RNA treated cells as well as on TSA (Trichostatin A) treated and untreated cells.

2015-04-22 | E-GEOD-65644 | biostudies-arrayexpress

ChIP-chip from human and mouse fetal brain

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-30 | E-GEOD-57358 | biostudies-arrayexpress