|
| Status |
Public on Mar 04, 2024 |
| Title |
WTCHG_72175193_D0_ChAdOx1_+ve |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
timepoint: D0
vaccine: ChAdOx1
naat result: +ve
age: 19.8
Sex: Female
participant number: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
RNA was ribodepleted and globin depleted using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 150bp paired-end sequencing (NovaSeq6000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
stage1
|
| Data processing |
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a).
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 9 or more samples.
Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (rpkm - reads per kilobase per million) for each gene for each sample
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Irina Chelysheva |
| E-mail(s) |
irina.chelysheva@ndm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
NDM
|
| Lab |
Centre for Human Genetics
|
| Street address |
Roosevelt Dr
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE228839 |
COVID-19 vaccination is associated with attenuation of inflammatory responses during breakthrough disease [Illumina RNA-Seq] |
| GSE228842 |
COVID-19 vaccination is associated with attenuation of inflammatory responses during breakthrough disease |
|
| Relations |
| BioSample |
SAMN34055598 |
| SRA |
SRX19854579 |
