|
| Status |
Public on Aug 29, 2020 |
| Title |
COVID_02_63y_male_NonICU |
| Sample type |
SRA |
| |
|
| Source name |
Leukocytes from whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: COVID-19
age (years): 63
Sex: male
icu: no
apacheii: unknown
charlson score: 2
mechanical ventilation: no
ventilator-free days: 28
dm: 0
hospital-free days post 45 day followup (days): 39
ferritin (ng/ml): 1060
crp (mg/l): unknown
ddimer (mg/l_feu): 1.03
procalcitonin (ng/ml): 0.37
lactate (mmol/l): unknown
fibrinogen: unknown
sofa: unknown
associated controlled-vocabulary terms: DOID:0080600 UBERON:0003101 CL:0000738 NCIT:C12529
cell type: leukocyte
tissue of origin: whole blood
sample type: primary cells
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10mL of whole blood collected from patients was filtered and RNA was isolated using LeukoLOCK Total RNA Isolation System.
TruSeq Stranded mRNA Library prep. Libraries were standardized to 2nM. Paired-end 2x50bp sequencing, using standard SBS chemistry (v3) on an Illumina NovaSeq6000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
C2
genes.ec.tsv
genes.tpm.tsv
|
| Data processing |
Basecalling via the standard Illumina Pipeline, version 1.8.2.
Trimming/Filtering for adapters and low quality via custom algorithm
Expression estimates via RSEM v1.3.0 under Python 2.7.15, using bowtie2-2.3.4.1. Executed command: rsem-calculate-expression --no-qualities --bowtie2 --bowtie2-k 200 --bowtie2-sensitivity-level sensitive --seed-length 20 --keep-intermediate-files --no-bam-output --paired-end [r1.fa.gz] [r2.fa.gz] [hg38 bowtie reference]
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited expression estimates, including non-normalized Expected Counts (EC), and normalized Transcripts Per Million (TPM)
|
| |
|
| Submission date |
Aug 28, 2020 |
| Last update date |
Aug 29, 2020 |
| Contact name |
Adolfo Ariel Jaitovich |
| E-mail(s) |
jaitova@amc.edu
|
| Organization name |
Albany Medical Center
|
| Department |
Molecular and Cellular Physiology
|
| Street address |
47 New Scotland Av
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12208 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE157103 |
Large-scale Multi-omic Analysis of COVID-19 Severity |
|
| Relations |
| BioSample |
SAMN15934956 |
| SRA |
SRX9033800 |
