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Immune and HCT116 RNA mixtures

ABSTRACT: These experiments were designed as a benchmark tool for deconvolution methods. 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs. RNA was extracted from the purified cell population, as well as from the HCT116 colon cancer cell line. RNAs from pure populations were then mixed in various proportions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64385 | GEO | 2016/02/18

SECONDARY ACCESSION(S): PRJNA270868

REPOSITORIES: GEO

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Similar Datasets

Immune and HCT116 RNA mixtures

Project description:These experiments were designed as a benchmark tool for deconvolution methods. 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs. RNA was extracted from the purified cell population, as well as from the HCT116 colon cancer cell line. RNAs from pure populations were then mixed in various proportions. RNA from HCT116 cells and FACS-sorted T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-), NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+), and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were mixed in various proportions.

2016-02-18 | E-GEOD-64385 | biostudies-arrayexpress

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Comparison of human plasmacytoid dendritic cells and monocyte-derived dendritic cells

Project description:Transcriptome analysis was conducted to investigate the gene expression profiles of pDCs using bulk RNA-sequencing (RNA-seq). Peripheral blood mononuclear cells (PBMCs) from healthy donors (n=3) were stained with lineage markers (CD3, CD14, CD16, CD19, and CD56), and pDCs were identified via flow cytometry (fluorescence-activated cell sorting [FACS]) based on the co-expression of IL-3R (CD123) and BDCA-2 (CD303). mDCs were identified using CD11c and sorted from the same PBMC donor as a control. After sorting, mRNA was extracted from the sorted cells, including mDCs and pDCs. The whole transcriptome profile was analyzed via RNA-seq.

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Gene expression analysis for CD56- T, NK, CD56+ T cells, and iNKT cells

Project description:A small subset of T cells also expresses kiler-cell immunoglobulin-like receptors (KIRs). We find that KIR+ T cells primarily reside in the CD56+ T population. However, little is known on how these cells are different from the conventional CD56- T, NK, and iNKT cells. We used microarray profiling to compare and determine the distinctive differences of CD56+ T cell and its KIR subsets when compared to the conventional CD56- T, NK and iNKT cells. Lymphocyte subsets were sorted from human peripheral blood mononuclear cells with FACSAriaII (BD Biosciences, San Jose, CA) using anti-CD3, anti-CD56, anti-CD14, anti-KIR2DL1, anti-KIR2DL2/3, anti-KIR3DL1 and anti-TCRValpha24 antibodies. The purity of CD3+CD56- T cells, CD3-CD56+ NK cells, CD3+CD56+ T cells, KIR-CD3+CD56+ T cells, and KIR+CD3+CD56+ T cells were more than 98% in all experiments. The purities of iNKT cells for TCRValpha24 and CD1d-tetramer were >95% and >90%, respectively. RNA pre-amplification, labeling and hybridization on Human Genome U133Plus 2.0 GeneChip array were performed in the St. Jude Hartwell Center for Bioinformatics & Biotechnology microarray core facility according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

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single cell RNAseq of peripheral CD4+ T cells in the context SARS-CoV-2 infection

Project description:CD4+ T cells play a fundamental role in host defenses against viruses by orchestrating B cell development and/or by directly targeting pathogens. This dataset aimed at understanding the molecular profile of CD4+ T cells in the context of an acute and severe SARS-CoV-2 infection. The analyzed patient was recruited at Henri Mondor University Hospital (AP-HP, Paris France) in March 2020, and required oxygen as treatment. Peripheral (CD14-CD56-CD123-CD19-CD3+CD4+CD45RA-PD-1high) T cells were FACS-sorted using a Sony MA900 in PBS/0.08% FCS. 1.105 cells were obtained and 20000 were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. The scRNA-seq libraries were generated using the Chromium Next GEM Single Cell V(D)J Reagent Kit v.1.1 with Feature Barcoding (10x Genomics) according to the manufacturer’s protocol. PBMCs were initially isolated from venous blood samples via standard density gradient centrifugation and used after cryopreservation at -150°C. Cells were thawed using RPMI-1640 (Gibco) 10% FBS, washed twice and incubated with fluorochrome-conjugated antibody cocktail and viable cells were identified using a LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific) incubated with conjugated antibodies used for cell sorting (CD3/CD4/CD14/CD19/CD45/CD56/CD123/PD-1) as well as a panel of barcoded TotalSeqC® antibodies (CD11c/CD21/CD27/CD38/CD49d/CD69/CD71/CD73/CD95/CD103/CD138/CD305/CD307d/CD307e/CXCR3/CXCR4/CXCR5/HLA-DR/ICOS/ITB7/LAG-3/NKG2D/TIM3). A single sort was performed for this patient and 5’-transcriptomic, VDJ and ADT libraries were sequenced .

2023-09-30 | E-MTAB-13321 | biostudies-arrayexpress

RUNX2-specific ChIP of human peripheral blood NK cells

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2022-06-03 | GSE172434 | GEO

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