Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A74788a3-2b10-414d-9a25-65d8b4c5e6f7 - samples

ABSTRACT: Single-cell CITE(cellular indexing of transcriptomes and epitopes)-seq from MDS (n = 2, MDS02 in 2 replicates). cDNA from 10x Genomics 3' V3.

PROVIDER: EGAD00001011281 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Specialized functions and sexual dimorphism explain the functional diversity of the myeloid populations during glioma progression

Project description:Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) used to dissect myeloid cell identities and states in murine experimental gliomas (GL261).

2022-12-06 | GSE220118 | GEO

Autonomous neutrophil ageing in the lung governed by the pulmonary microbiome

Project description:We used cellular indexing of transcriptomes and epitopes-based single cell RNA sequencing (CITE-scRNAseq) coupled with adoptive transfer approaches to determine tissue contribution to neutrophil diversity.

2020-07-15 | GSE154406 | GEO

CITE-seq analysis of mouse LSK cells

Project description:We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of the LSK compartment of TdT-reporter and TdT-fate mapping mice, in order to elucidate the heterogeneity and developmental trajectories within the MPP (lymphoid-primed multipotent progenitor) and HSC (hematopoietic stem cell) compartments.

2022-03-27 | GSE145491 | GEO

Single cell analysis of CD1a-restricted Group A streptococcus (GAS)-reactive peripheral and cutaneous T cells

Project description:Skin and blood single cell RNA sequencing datasets of IL-22- and IFNγ-secreting CD1a-reactive GAS-responsive T cells were generated from four healthy skins, five healthy PBMCs and three psoriatic PBMCs. Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we measured T cell specific functional states at both protein and transcriptome levels.

2023-07-11 | GSE206326 | GEO

Single cell profiling of CD4+ T cells from follicular lymphoma, diffuse large B cell lymphoma and tonsilar samples

Project description:Tumor-infiltrating regulatory T cells contribute to an immunosuppressive tumor microenvironment. We applied single-cell RNA sequencing (scRNA-seq) , TCR sequencing combined with cellular indexing of transcriptomes and epitopes (CITE-seq) on CD4 T cells to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), compared with non-malignant tonsillar tissue.

2023-09-12 | GSE242756 | GEO

CITE-seq of LSK cells from aged mice after long-term iron chelator regimen

Project description:We found that iron chelation restored functional defects in aged HSC, including engraftment potential and platelet bias. To gain molecular insights into iron-dependent mechanism for sustaining HSC identity during aging, we performed Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) with lineage (Lin)− Sca-1+ cKit+ (LSK) cells isolated from aged mice after long-term regimens with iron chelator Deferoxamine or vehicle control.

2024-05-02 | GSE232022 | GEO

6ab815bf-6b55-4196-8d32-18baabf23a77 - samples

Project description:Single-cell RNA sequencing from CH (n = 2), MDS (n = 6, MDS02 in 2 replicates) and AML (n = 1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8, U2AF1 n = 1). cDNA from 10x Genomics 3' V3.

| EGAD00001011283 | EGA

cb0eb12f-8a50-45f3-b426-afb7347cd6d2 - samples

Project description:In this study, we aimed to assess RNA expression and surface antigen expression of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level. For this purpose, we performed cellular indexing of transcriptomes and epitopes (CITE-seq) of primary leukemia samples from four CK-AML patients.

| EGAD00001011171 | EGA

Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

Project description:The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.

2022-06-13 | GSE200417 | GEO

Human Early Postnatal Thymus [CITE-seq]

Project description:Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Assay for Transposable-Accessible Chromatin (ATAC-seq). We generated age-matched 4–5-month-old postnatal thymus datasets for both male and female donors, and describe signaling and cell-cell interaction networks in sequential thymocyte developmental niches. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.

2024-08-30 | GSE264587 | 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