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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
E-mail(s) jvarner@ucsd.edu
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
Relations
BioProject PRJNA787287
SRA SRP349862

Download family Format
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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