|
| Status |
Public on Mar 04, 2024 |
| Title |
sample28_CT_MenACWY_-ve |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
timepoint: CT
vaccine: MenACWY
naat result: -ve
age: 40
Sex: Male
participant number: 19
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0) and at SARS-CoV-2 diagnosis (CT). 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).
PCR-cDNA libraries were prepared using the SQK-PCS110 PCR-cDNA-sequencing kit following the standard Oxford Nanopore Technologies (ONT) protocol. Samples were barcoded (#1-8) and sequenced on PromethION. 2 samples were loaded per flow cell (15 ng each), with the paired samples run together and the unpaired samples randomly split into pairs
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Description |
stage1
|
| Data processing |
The base calling and demultiplexing were performed live using original ONT software.
Reads were aligned to the reference transcriptome (version GRCh38) using minimap2 (secondary score ratio -p 0.99)
The transcript abundances were estimated from the output bam files using Salmon in alignment-based mode
Transcripts detected in less than 50 % of the samples from at least one of the study groups were removed. Ribosomal RNA (rRNA), mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (counts per million) for each transcript for each sample
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Irina Chelysheva |
| E-mail(s) |
[email protected]
|
| 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 |
GPL26167 |
| Series (2) |
| GSE228840 |
COVID-19 vaccination is associated with attenuation of inflammatory responses during breakthrough disease [long-read RNA-Seq] |
| GSE228842 |
COVID-19 vaccination is associated with attenuation of inflammatory responses during breakthrough disease |
|
| Relations |
| BioSample |
SAMN34058666 |
| SRA |
SRX19856978 |
