ATAC-seq of purified immune cell populations
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE125164 | GEO | 2022/12/10
REPOSITORIES: GEO
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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.
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Project description:Bulk ATAC-Seq was performed on human cord-blood derived hematopoietis popuations using the following markers:
LT-HSC; CD34+CD38-CD45RA-CD90+CD49f+
ST-HSC; CD34+CD38-CD45RA-CD90-CD49f-
MLP; CD34+CD38-CD45RA+
CMP; CD34+CD38+ CD10-CD45RA-Flt3+CD71-
GMP; CD34+CD38+ CD10-CD45RA+ CD71-
MEP; CD34+CD38+ CD10-CD45RA-Flt3-CD71+
T cell; CD3+CD19-
B cell; CD19+CD3-
NK cell; CD56+CD3-CD19-CD14-
Granulocyte; CD14+CD15+CD3-CD19-
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DC; CD11c+CD45+
Erythroid cell; CD71+GPA+
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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.
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