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Series GSE190494 Query DataSets for GSE190494
Status Public on Apr 12, 2023
Title Nanostring GeoMx digital spatial profliing of myeloid cells from COVID-19 and normal lung
Organisms Homo sapiens; blank sample
Experiment type Expression profiling by high throughput sequencing
Summary To determine definitively whether lung myeloid cells exhibit a pro- or anti-inflammatory signature in COVID-19 disease, we performed digital spatial profiling using the nanoString GeoMx ImmuneOncology plus COVID-19 platform on CD68+ macrophages, myeloperoxidase+ granulocytes and cytokeratin+ epithelium in normal and COVID-19 lung tissue specimens, collecting RNA expression data for each type within 6-8 regions of 5mM tissue sections. One COVID-19 lung tissue yielded minimal sequence data and was excluded from analysis. A volcano plot and heat map of differentially expressed genes within macrophages demonstrate that COVID-19 lung macrophages when compared with normal lung macrophages exhibit a largely alternatively activated, wound-healing signature characterized by expression of the alternatively active macrophage marker CD163, complement/coagulation genes (C1QA, C1QB, THBS1, C1S, C1R), IL6 signaling (STAT2, STAT1) and wound healing (COL3A1, COL6A3), but also interferon response signatures (ISG15, OAS3, IFITM2, IFI6, HLA-A, HLA-B, HLA-C) (Fig. 3H-J). As one of the tissues used for macrophage spatial profiling was from a patient was positive for the virus at the time of death, we compared the expression profiles of virus+ and virus- specimens and found that macrophages in virus+ tissues predominantly expressed an interferon-associated signature
Overall design 3 COVID-19 samples and 1 normal lung samples were analyzed by nanoString GeoMX digital Spatial profiling. Each of 6-8 regions of interest per tissue were profiled with 3 cell type specific markers : CD68 for macrophages, Myeloxperoxidase for neutrophils and cytokeratin for epithelial cells as well as DNA specific marker.
Contributor(s) Varner JA, Ghebremedhin A, Fisch K
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Submission date Dec 08, 2021
Last update date Apr 12, 2023
Contact name Judith Varner
Phone 8588220086
Organization name University of California, San Diego
Department Moores Cancer Center
Street address 3855 Health Sciences Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093-0819
Country USA
Platforms (2)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL29487 Illumina NovaSeq 6000 (blank sample)
Samples (95)
GSM5724650 No template DSP-1001660005232-A-A01
GSM5724651 CD68 DSP-1001660005232-A-A02
GSM5724652 PanCK DSP-1001660005232-A-A03
BioProject PRJNA787287
SRA SRP349862

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE190494_DSP_read_count_summary.csv.gz 2.9 Kb (ftp)(http) CSV
GSE190494_Q3_Normalized_Data1.csv.gz 755.5 Kb (ftp)(http) CSV
GSE190494_Varner_Covid-19_Study_20210316T0020_LabWorksheet1.txt.gz 1.7 Kb (ftp)(http) TXT
GSE190494_Varner_Covid-19_Study_20210316T0020_SeqCodeIndices.csv.gz 1.6 Kb (ftp)(http) CSV
GSE190494_seq_template-Varner_Nanostring.xlsx 65.9 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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