NanoString Analysis of Dendritic Cell Transcriptome

Total RNA was extracted from DC using a RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. NanoString analysis was similarly performed using a nCounter^® Human Immunology v2 Panel (Catalogue number XT-CSO-HIM2-12, NanoString Technologies) as described.^{21 (link),43 (link)} Gene expression data were log2-transformed and normalized to the geometric mean expression of 15 house-keeping genes using the nSolver software platform 4.0 (NanoString Technologies). Pathways were analyzed using Ingenuity Pathway Analysis (IPA) software (Qiagen).

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Macedo C., Tran L.M., Zahorchak A.F., Dai H., Gu X., Ravichandran R., Mohanakumar T., Elinoff B., Zeevi A., Styn M.A., Humar A., Lakkis F.G., Metes D.M, & Thomson A.W. (2020). Donor-derived regulatory dendritic cell infusion results in host cell cross-dressing and T cell subset changes in prospective living donor liver transplant recipients. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 21(7), 2372-2386.

Publication 2020

RNeasy Mini Kit nCounter® Human Immunology v2 Panel nSolver software platform 4.0 Ingenuity Pathway Analysis (IPA) software

Gene expression House keeping genes Human

Corresponding Organization : University of Pittsburgh

Other organizations : St. Joseph's Hospital, St. Joseph's Hospital and Medical Center

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Variable analysis

independent variables

Total RNA extraction from DC using a RNeasy Mini Kit (Qiagen)

dependent variables

Gene expression data (log2-transformed and normalized to the geometric mean expression of 15 house-keeping genes)

control variables

Manufacturer's instructions for RNeasy Mini Kit (Qiagen)
NCounter^® Human Immunology v2 Panel (Catalogue number XT-CSO-HIM2-12, NanoString Technologies)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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