|
| Status |
Public on May 20, 2022 |
| Title |
ChAd-12_I-D0 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
age: 34
gender: Male
vaccine: 1st dose, ChAdOx1
cell type: PBMCs
|
| Growth protocol |
Blood samples were collected from individuals both prior and after vaccinations.
|
| 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.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
May 20, 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 (2) |
| GSE201533 |
Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [RNA_seq] |
| GSE201535 |
Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron |
|
| Relations |
| BioSample |
SAMN27777690 |
| SRA |
SRX14999120 |
