Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CITE-seq of in vitro control and memory-like human NK cells

ABSTRACT: Peripheral blood NK cells were cultured into either control or cytokine-induced memory-like NK cells as described in PMID: 32614951. After differentiation, cells were labeled with hashtag antibodies and cite-seq antibodies and control and memory-like NK cells were combined and loaded onto the 10x Genomics Chromium Instrument a the McDonnell Genome Institute at Washington University School of Medicine. The following samples were analyzed to develop a classification tool for unbiased identification of memory-like NK cells in a bulk single-cell RNA-seq population.

ORGANISM(S): Homo sapiens

PROVIDER: GSE185989 | GEO | 2022/02/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

scRNAseq of isolated fetal liver erythroid progenitor cell subpopulations, and CITE-seq of mouse fetal liver erythroid progenitors

Project description:We used scRNAseq to profile CD71/CD24low fetal liver erythroid progenitor cells isolated by 2 distinct methods: FACS and immunomagnetic isolation. Cells from both isolation methods were hashtagged using Biolegend mouse hashtag antibodies and library prepped together on the 10X chromium platform with the 3'RNA v3 kit. We also performed CITE-seq to profile proteogenomic expression of CD117 and CD71 on lineage-depleted mouse fetal liver erythroid progenitor cells. CITE-seq was performed through a separate library prep on the 10X chromium platform with the 3'RNAv3 kit.

2021-11-12 | GSE188287 | GEO

CITE-seq of CAR-NK cells

Project description:CITE-seq of CAR-NK cells

| PRJNA915004 | ENA

CITE-seq of in vitro control and memory-like human NK cells

Project description:CITE-seq of in vitro control and memory-like human NK cells

| PRJNA771661 | ENA

Titration of 124 antibodies using CITE-Seq on human PBMCs

Project description:Single-cell RNA-sequencing (scRNA-Seq) is widely used to characterize immune cell populations. However, mRNA levels correlate poorly with expression of surface proteins, which are well established to define immune cell types. CITE-Seq (cellular indexing of transcriptomes and epitopes by sequencing) utilizes oligonucleotide-tagged antibodies to simultaneously analyze surface phenotypes and transcriptomes. Considering the high costs of adding surface phenotyping to scRNA-Seq, we aimed to determine which of 188 tested CITE-Seq antibodies can detect their antigens on human peripheral blood mononuclear cells (PBMCs), a commonly interrogated cell population in immunology, and find the optimal concentration for staining. The recommended concentration was optimal for 76 antibodies, whereas staining quality of 7 antibodies improved when the concentration was doubled. 33 and 8 antibodies still worked well when the concentration was reduced to 1/5 or 1/25, respectively. 64 antigens were not detected at any antibody concentration. Optimizing the antibody panel by removing antibodies not able to detect their target antigens and adjusting concentrations of the remaining antibodies could enable a cost reduction of almost 50%. In conclusion, our data are a resource for building an informative and cost-effective panel of CITE-Seq antibodies and use them at their optimal concentrations in future CITE-seq experiments on human PBMCs.

2022-09-18 | GSE213282 | GEO

Strategies for optimizing CITE-seq for human islets and other tissues

Project description:Defining the immunological landscape of human tissue is an important area of research, but challenges include the impact of tissue disaggregation on cell phenotypes and the low abundance of immune cells in many tissues. Here, we describe methods to troubleshoot and standardize Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) for studies involving enzymatic digestion of human tissue. We tested epitope susceptibility of 92 antibodies commonly used to differentiate immune lineages and cell states on human peripheral blood mononuclear cells following treatment with an enzymatic digestion cocktail used to isolate islets. We observed CD4, CD8a, CD25, CD27, CD120b, CCR4, CCR6, and PD1 display significant sensitivity to enzymatic treatment, effects that often could not be overcome with alternate antibodies. Comparison of flow cytometry-based CITE-seq antibody titrations and sequencing data supports that for the majority of antibodies, flow cytometry accurately predicts optimal antibody concentrations for CITE-seq. Comparison by CITE-seq of immune cells in enzymatically digested islet tissue and donor- matched spleen not treated with enzymes revealed little digestion-induced epitope cleavage, suggesting increased sensitivity of CITEseq and/or that the islet structure may protect resident immune cells from enzymes. Within islets, CITEseq identified immune cells difficult to identify by transcriptional signatures alone, such as distinct tissue-resident T cell subsets, mast cells, and innate lymphoid cells (ILCs). Collectively this study identifies strategies for the rational design and testing of CITE-seq antibodies for single-cell studies of immune cells within islets and other tissues.

2023-02-12 | GSE224767 | GEO

CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

Project description:Vitamin D deficiency is a risk factor for multiple sclerosis (MS) and is correlated with disease activity and progression. Vitamin D treatment has emerged as potentially protective, even though results from randomized controlled trials are conflicting. Here, we used single-cell RNA-seq (scRNA-seq) coupled with barcoded antibodies targeting surface markers (CITE-seq) to discover candidate genes and pathways regulated in PBMC subpopulations from MS patients treated with high-dose vitamin D (n=5) or placebo (n=5). Best candidates were combined with genes involved in immune function and vitamin D metabolism for validation in a new cohort (n=8 in each group) by high-throughput qPCR (HT-qPCR) in naive CD4, Th1, Th17, Treg, naive CD8, memory and naive B cells, and MAIT cells, sorted by FACS. CITE-seq showed no significant changes in the proportions of these subpopulations in vitamin D-treated patients. Of the 92 candidate genes revealed by CITE-seq, differential expression of five genes (UXT, SNRPN, SUB1, GNLY and KLF6) was validated by HT-qPCR. CITE-seq also revealed the regulation of several pathways by vitamin D in naive and memory B cells, including MAPK, TLR and interleukin pathways, that contribute to counteract EBV-induced resistance to apoptosis through inhibition of the NF-kB pathway.

2023-10-05 | GSE239626 | GEO

Single cell 5’ transcript, TCRαβ enriched, and Cell hashing/CITE-seq library preparation on the 10x chromium, and sequencing

Project description:Single cells from human colorectal cancer and normal adjacent colon of 16 patients were used for single-cell RNA-seq, TCR-seq, CITE-seq and Cell hashing. In brief, single cells were incubated for 3h with or without PMA/Ionomycin, and were treated with Cell hashing and CITE-seq antibodies to distinguish samples, stimulation/non-stimulation, and cell surface proteins. Sorted viable CD3+TCRαβ+ single cells were loaded into 10x genomics ChromiumTM controller to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library was sequenced with Illumina Novaseq. The single cell TCR enriched library was sequenced with Illumina Miseq using 150 paired-end reads. HTO/ADTs from Cell hashing or CITE-seq were amplified using specific primers that append P5 and P7 sequences for illumina sequencing (Miseq or Nextseq). All fastq files were demultiplexed. Cell hashing and CITE-seq barcodes are available in attached text files. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of independent experiments at May 29, June 16, June 23, and Aug 13, 2019. Details are available in Masuda et al., bioRxiv, 2020, The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.

2022-03-02 | E-MTAB-9455 | biostudies-arrayexpress

Vaccine-induced tissue resident memory T cells and antibodies synergize to prevent mucosal HIV infection [CITE-seq]

Project description:Vaccine-induced tissue resident memory T cells and antibodies synergize to prevent mucosal HIV infection [CITE-seq]

| PRJNA574940 | ENA

Natural killer cell proliferation requires canonical IRE1 function during viral infection (CITE-Seq)

Project description:The unfolded protein response (UPR) aims to restore ER homeostasis under conditions of high protein folding load, a function primarily serving secretory cells. Additional, non-canonical UPR functions have recently been unraveled in immune cells. We addressed the function of the inositol-requiring-enzyme 1 (IRE1) signaling branch of the UPR in NK cells in homeostasis and microbial challenge. Cell-intrinsic compound deficiency (DKO) of IRE1 and its downstream transcription factor XBP1 in NKp46 + NK cells, did not affect basal NK cell homeostasis, or overall outcome of viral MCMV infection. However, mixed bone marrow chimeras revealed a competitive advantage in the proliferation of IRE1 sufficient Ly49H + NK cells after viral infection. CITE-Seq analysis confirmed strong induction of IRE1 early upon infection, concomitant with the activation of a canonical UPR signature. Therefore, we conclude that cell-intrinsic IRE1/XBP1 activation is required for NK cell proliferation early upon viral infection, as part of a canonical UPR response.

2023-10-27 | GSE236820 | GEO

Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq]

Project description:NK cells are innate lymphoid cells that protect the host against malignant and infected cells. Activation with the cytokines IL-12, IL-15, and IL-18 induces NK cells to differentiate into memory-like NK cells that have enhanced function compared to conventional NK (cNK) cells. However, mechanisms governing their biology and whether all cNK cells become memory-like are unclear. We identified that IL-12/15/18 activation results in two main fates: reprogramming into enriched memory-like (eML) or priming into effector (eff)cNK cells. eML NK cells have distinct epigenetics, phenotype, and enhanced function (IFNγ, cytotoxicity) compared to cNK and effcNK cells. In contrast, effcNK cells transcriptionally and epigenetically resemble cNK cells. Furthermore, we identify that within cNK cells CD56bright and CD56dim NK cells are the origin of distinct subsets of eML NK cells. Moreover, these two subsets of eML NK cells persist within patients receiving ML NK cell therapy for several months. Thus, IL-12/15/18 activation of NK cells results in multiple cell fates, with epigenetic and transcriptional mechanisms orchestrating eML NK cell differentiation and function. These mechanistic insights provide new strategies to enhance NK cellular therapy.

2024-06-28 | GSE264696 | 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