|
Status |
Public on Jan 25, 2022 |
Title |
Beta-S02_2nd |
Sample type |
SRA |
|
|
Source name |
PBMCs
|
Organism |
Homo sapiens |
Characteristics |
age: 80 gender: Female diseas state: COVID-19_Beta varient geographical location: Ischgl, Austria cell type: PBMC
|
Growth protocol |
Blood samples were collected from the COVID-19 patients infected by Beta variant and the Naïve vaccinated individuals.
|
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 using a Maxwell RSC simply RNA Blood purification kit. 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 |
Nov 17, 2021 |
Last update date |
Jan 25, 2022 |
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) |
GSE189039 |
Prior BNT162b vaccination enhances interferon-JAK-STAT regulated antiviral programs in hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant |
|
Relations |
BioSample |
SAMN23243331 |
SRA |
SRX13158421 |