|
| Status |
Public on Sep 02, 2020 |
| Title |
C9_02_nCOV_OIRRA_Lib43_20200423 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
material: FFPE
age: 88
Sex: M
diagnosis: COVID-19
topography: Lung, left superior lobe
time post mortem (h): 13
bmi: 28
pre-existing pulmonary condition(s): 0
antiviral medication yes (1) / no (0): 1
anamnestic symptom onset to death (days): 19
hospitalisation time (days): 2
histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes): 1
histology - dad (1 = yes; 0 = no): 0
dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic): -
intraalveolar edema (1 = yes; 0 = no): 0
intraalveolar hemorrhage (1 = yes; 0 = no): 0
neutrophils (1 = few; 2 = moderate; 3 = numerous): 1
sars-cov-2 genomes / 10^6 rnasep copies: 85137.3755827618
hypertension: 1
cvrf: 1
copd: 0
smoker: 0
diabetes: 0
malignant tumor: 1
cough: 1
fever: 0
dyspnea / tachypnea: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RecoverAll Total Nucleic Acid Isolation Kit (Cat No. AM1975, Thermo Fisher Scientific, Waltham, MA, USA)
Oncomine Immune Response Research Assay (OIRRA, Cat No. A32881, Thermo Fisher Scientific, Waltham, MA, USA)
targeted RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 XL |
| |
|
| Description |
C9_02_nCOV_OIRRA_Lib43_20200423_IonXpress_043
processed data file:
user_S5-0093-279-OIRRA_2_20200423_581.bcmatrix.csv
user_S5-0093-279-OIRRA_2_20200423_581.mean_hk_scaled_log2_count.csv
user_S5-0093-279-OIRRA_2_20200423_581.rpm.bcmatrix.csv
|
| Data processing |
De-multiplexing and gene expression level quantification were performed with the standard setting of the ImmuneResponseRNA plugin, provided as part of the OIRRA.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Ronny Nienhold |
| Organization name |
Cantonal Hospital Baselland
|
| Department |
Institute of Pathology
|
| Street address |
Mühlemattstrasse 11
|
| City |
Liestal |
| ZIP/Postal code |
4410 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24014 |
| Series (1) |
| GSE151764 |
Two distinct immunopathological profiles in lungs of lethal COVID-19 |
|
| Relations |
| BioSample |
SAMN15097552 |
| SRA |
SRX8466986 |
