|
| Status |
Public on May 01, 2021 |
| Title |
B_342_Seronegative |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
age: 49
gender: Male
diseas state: highly exposed, Seronegative
severity: Seronegative, highly exposed
location: Austria: Ischgl
cell type: PBMC
|
| Growth protocol |
Blood samples were collected from the healthy subjects, Seronegative subjects and COVID-19 patients.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated with TRIzol reagent.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples
|
| |
|
| Submission date |
Dec 02, 2020 |
| Last update date |
May 04, 2021 |
| Contact name |
Hye Kyung Lee |
| E-mail(s) |
hyekyung.lee@nih.gov
|
| Phone |
301-435-6635
|
| Organization name |
National Institutes of Health (NIH)
|
| Department |
National Institute of Diabetes and Digestive and Kidney (NIDDK)
|
| Lab |
Laboratory of Genetics and Physiology
|
| Street address |
8 CENTER DR RM 107
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE162562 |
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community |
|
| Relations |
| BioSample |
SAMN16983207 |
| SRA |
SRX9621447 |
