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Sample GSM4980795 Query DataSets for GSM4980795
Status Public on Apr 11, 2021
Title D20 | 004 | PanCK-
Sample type other
 
Source name LUL
Organism Homo sapiens
Characteristics infection: SARS-CoV-2 infected
x coordinate: 21027.27539
y coordinate: 34019.79297
aoi surface area: 268469.500025
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_08.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 3.053363437
CD4 2.930716659
PanCk 2.851407906
PD-L1 1.009151129
CD45 4.116519019
Fibronectin 7.488731202
CTLA4 2.602780813
SMA 6.087834202
CD20 2.420870476
Beta-2-microglobulin 2.297896777
CD68 4.10501856
PD-1 1.672823996
Ki-67 4.381088436
CD56 3.418482873
CD3 3.005282101
GZMB 3.676615942
CD11c 4.134605015
HLA-DR 4.023215176
Cathepsin L/V/K/H 3.901930925
ACE2 1.660536396

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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