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Sample GSM4980790 Query DataSets for GSM4980790
Status Public on Apr 11, 2021
Title D20 | 002 | PanCK+
Sample type other
 
Source name LUL
Organism Homo sapiens
Characteristics infection: SARS-CoV-2 infected
x coordinate: 35530.3125
y coordinate: 28738
aoi surface area: 37244.561637
binding density: 0.11
segment: PanCK+
segment: Alveolar
race: White
ethnicity: not provided
Sex: F
age: 65-70
organ failure: Lung, heart
s/s to death (days): 1
Extracted molecule other
Extraction protocol [sample isolation protocol] Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.
Sample extraction was performed according to NanoString GeoMx manufacturer instructions. Slides were stained with antibody panels and a SARS-CoV-2 panel spike-ins, all consisting of RNA-ISH probes conjugated with a UV-photocleavable barcodes; along with Syto13, Anti-PanCK, and Anti-CD45 morphological markers. ROIs were selected based on pathologist annotation of morphology, PanCK signal, and S-gene RNAScope from sequential slides. ROIs were segmented into PanCK+ and PanCK- for LUL samples. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform.
Label n/a
Label protocol n/a
 
Hybridization protocol Oligonucleotides were then hybridized to fluorescent barcodes and run through the nCounter MAX analysis system to generate raw digital counts. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Scan protocol Oligonucleotides were then hybridized to fluorescent barcodes and run through the nCounter MAX analysis system to generate raw digital counts. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Description raw data file: 20201004_P1001250001721A_P1001250001721A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc
Data processing The raw counts were inputted into the DSP for calibration (adjusting for oligo-barcode binding efficiency) and for generation of a protein expression matrix; this matrix was subsequently normalized to internal spike-in positive controls (ERCC) to account for system variation. The calibrated and ERRC-normalized expression matrix was then normalized to the geometric mean of housekeeping genes99 as follows: first, the geometric mean of three housekeeping genes, histone H6, GAPDH, and S6, was calculated for each AOI; next, normalization factors were calculated as the geometric mean in each AOI dividing by the geometric mean of geometric means across all AOIs; finally, raw expression values were divided by the calculated normalization factors to give normalized protein expression levels.
 
Submission date Dec 18, 2020
Last update date Apr 11, 2021
Contact name Samouil Farhi
Organization name Broad Institute of MIT and Harvard
Street address 415 Main St.
City Cambridge
State/province Massachusetts
ZIP/Postal code 02142
Country USA
 
Platform ID GPL29514
Series (2)
GSE163529 A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [protein levels]
GSE163530 A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Data table header descriptions
ID_REF
VALUE Normalized counts (from NormalizedCountMatrix.xlsx)

Data table
ID_REF VALUE
CD8 2.706710853
CD4 2.213109738
PanCk 4.45542455
PD-L1 1.252991669
CD45 2.846739829
Fibronectin 5.855865491
CTLA4 1.221167043
SMA 4.46758816
CD20 1.18277392
Beta-2-microglobulin 1.144424642
CD68 4.015453111
PD-1 1.247899498
Ki-67 5.608487327
CD56 2.248174632
CD3 1.995170747
GZMB 3.093167219
CD11c 4.037579203
HLA-DR 3.828374305
Cathepsin L/V/K/H 3.733275156
ACE2 1.962095533

Total number of rows: 77

Table truncated, full table size 1 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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