Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of peripheral blood mononuclear cells from Huntington's disease patients and controls

ABSTRACT: Transcriptional dysregulation is among the most prominent molecular alterations in Huntington’s disease. It is not confined to brain but is also extended to peripheral tissues and cells, enabling minimally invasive screens aimed at identifying transcriptional surrogates of the health status in HD mutation carriers. In this study, we applied single-cell RNA-seq in peripheral blood mononuclear cells (PBMCs) to determine those cellular compartments that accumulate the most prominent gene expression changes as potential sources of reliable biomarkers.

INSTRUMENT(S): Illumina NovaSeq 6000, Chromium 10xGenomics

ORGANISM(S): Homo sapiens

SUBMITTER: Luis Valor

PROVIDER: E-MTAB-15129 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA Single Cell Sequencing of Colorectal Liver Metastasis regarding their Histopathological Growth Pattern

Project description:Molecular characterization of single cells in Colorectal Cancer Liver Metastases (CRCLM) and corresponding healthy liver tissue focusing on the comparison between the two main histopathological growth patterns (HGPs): desmoplastic HGP (dHGP) and replacement HGP (rHGP) with the intent to identify possible biomarkers or treatment targets especially for the more aggressive replacement HGP.

2023-01-05 | E-MTAB-12022 | biostudies-arrayexpress

iPS2-10X-seq experiment on specific clones targeting with an shRNA either SMAD2 or B2M

Project description:We transfected hiPSCs WTC11 with specific shRNAs targeting SMAD2 or B2M. hiPSCs transfected were selected, cultured, and clones were picked and expanded for follow-up validations. Among these validations, we obtained this scRNAseq dataset. We cultured hiPSCs and differentiated them into cardiac organoids for 7.5 days with and without Tetracycline treatment. This experiment allowed to identify the role of SMAD2 during cardiac differentiation.

2025-10-27 | E-MTAB-15307 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snRNA-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11225 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snATAC-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11226 | biostudies-arrayexpress

scRNAseq of AKP Mex3a KO mouse colorectal organoids in FOLFIRI treatment

Project description:Mex3a is an RNA binding protein of unknown function. To elucidate the contribution of Mex3a to tumoral heterogeneity, Mex3a KO organoids engineered by CRISPR were sequenced in three different conditions. Live organoids (DAPI negative) were sorted in Control, after 2 days of FOLFIRI and after 5 days of treatment. Two WT organoids (parental and a derived clone) and two KO (KO1 and KO2, two independent clones) were used for this experiment.

2022-05-16 | E-MTAB-11146 | biostudies-arrayexpress

Single cell RNA sequencing of intestinal NKp46+ innate lymphoid cells (ILCs) from Hif1a(fl/fl) and Ncr1(Cre)Hif1a(fl/fl) mice

Project description:The unbiased approach to determine transcriptional profiles of sorted NKp46+ cells from the small intestine of WT and HIF-1α KO mice.

2021-12-18 | E-MTAB-11238 | biostudies-arrayexpress

Single-cell RNA-seq of human breast tumor samples with exhausted and non-exhausted immune environments

Project description:Fresh human breast tumor tissue was dissociated into single cells and viably frozen. Patient samples were annotated as having an ""exhausted"" or ""non-exhausted"" immune environment based on CyTOF characterization of T cell phenotypes (Wagner et al, Cell 2019). 14 samples (7 exhausted, 7 non-exhausted) were selected for scRNA-seq (without prior cell type enrichment) with the goal to compare the two immune environment types and to comprehensively characterize exhaustion-associated features of the tumor microenvironment.

2023-08-25 | E-MTAB-10607 | biostudies-arrayexpress

Single cell RNA-seq of human synovial joints from healthy donors

Project description:Human synovial Single cell RNA-seq was performed on three tissue samples from healthy donors. This experiment was done to explore the heterogeneity of cells in healthy human synovial joint and enabled the comparison of cellular states and composition to those of publicly available single cell RNA-seq datasets from psoriatic arthritis and rheumatoid arthritis patients. Human synovial cells were loaded immediately after tissue dissociation with up to 25,000 cells in a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as paired end (PE) 150 bp by Illumina sequencing to 65-80% saturation. Reads were mapped to the GRCh38 human genome (GENCODE) using the 10x Genomics Cell Ranger pipeline (7.2.0).

2024-08-06 | E-MTAB-14339 | biostudies-arrayexpress

Proteogenomic Profiling Reveals Functional Microproteins in T Cells

Project description:Noncanonical micropeptides, i.e., polypeptides mostly under 10 kDa, are encoded by genomic sequences that have been previously annotated as noncoding but now known as small open reading frames (sORFs). The recent identification of microproteins encoded by sORFs has provided evidence that many sORFs encode functional microproteins that play crucial roles in various biological processes. T cell activation is a critical biological process for adaptive immune response. Understanding key players in this process will allow us to decipher the complex mechanisms as well as develop immunotherapy for treating a wide range of diseases. Although there have been extensive studies on canonical proteins in T cell activation, the microproteins in T cells and their roles have been uncharted water to date. In this study, we combined nascent proteomics and quantitative proteomics to identify 411 novel microproteins in primary human T cells, including 83 nascent microproteins that are defined as newly synthesized polypeptides emerged during the translation of mRNA. We activated the T cell function with either PMA/Ionomycin (distal activation) or CD3/CD28 activating antibodies (proximal activation), and obtained a comprehensive canonical protein and microprotein profiles to pinpoint common and distinct differentially expressed proteins under these two activation conditions. After experimental testing, three microproteins numbered T1, T2 and T3 were found to be functional in regulating T cell activation. Bioinformatic and proteomic analyses suggested that T1 was functional related to immune as negative feedback to T cell activation. Our study not only established an integrated approach to uncover and elucidate novel microproteins but also highlight the significant role of microproteins in regulating T cell activation.

2025-08-04 | PXD058995 | Pride

Single-cell RNA-seq (10x Chromium V3) of heterogeneous spheres consisting of melanoma cell line and two types of human primary dermal fibroblasts.

Project description:Photo-damage represents an important aspect of cutaneous carcinogenesis. The photo-damaged microenvironment significantly facilitase progression of malignant melanoma. Therefore human primary dermal fibroblasts from photo-damaged adult skin and juvenile sun-protected skin were isolated and expanded as described by Dvorankova et al. (PMID: 29675784). Low passage fibroblasts were mixed in suspension (in ratio 1:1) with G361 malignant melanoma cell line (CVCL_1220). Using the hanging drop technique (PMID: 29786551), the melanoma/fibroblast spheres containing 50,000 cells per sphere were formed during the next 72 hours. The organoids were consequently maintained for another 2 days in non-adhesive culture wells in complete DMEM culture medium. At this time, heterogeneous spheres were harvested for immunohistochemical analysis or for further invasion studies. Single-cell suspensions from heterogeneous spheres were analysed by single-cell RNA sequencing (10x Chromium V3) to reveal the transcriptional heterogeneity of model cell populations under given conditions with emphasis on the features of dermal fibroblasts exposed to the influence of malignant melanoma.

2021-05-12 | E-MTAB-9216 | 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