Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA603604

PRJNA603604: Diversity of peripheral blood human NK cells identified by single cell RNA sequencing

Source: NCBI / GSE144430
Submission Date: Jan 28 2020
Release Date: Jan 29 2020
Update Date: Apr 20 2020

Summary: Human Natural Killer (NK) cells in peripheral blood perform many functions but classification of specific subsets has been a long-standing problem. Here, we report single-cell RNA sequencing of NK cells from healthy CMV-negative donors, comparing gene expression in unstimulated and IL-2 activated cells. Unsupervised clustering identified seven NK cell subsets. Three resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which were CD56neg; a population exhibiting an in-vivo cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2, and finally, a small population, with low ribosomal expression, down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Human cytomegalovirus positive donors also included a higher frequency of adaptive NK cells. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analysing NK cell responses in health and disease.

Overall Design: scRNAseq of sorted NK cells from one healthy individual

GEN Datasets:
GEND000132
Strategy:
Species:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood collected into EDTA-coated tubes (fisher scientific) using density gradient centrifugation (Ficoll-Paque Plus; Amersham Pharmacia Biotech). Primary human NK cells were isolated using negative magnetic bead selection (Miltenyi Biotec or Stemcell Technologies).
Treatment Protocol: -
Extract Protocol: Individually-barcoded single cell RNA-seq libraries were prepared using the Chromium Single Cell Controller
Library Construction Protocol: Chromium Single Cell 3'Library & Gel Bead Kit v2 kit (10x Genomics, Pleasanton, CA). All steps were carried out according to the manufacturers'instructions.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NextSeq 500
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing.
Blood advances . 2020-04-01 [PMID: 32271902]