|
Status |
Public on Mar 04, 2024 |
Title |
sample32_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: 32 Sex: Male participant number: 23
|
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 |
SAMN34058662 |
SRA |
SRX19856982 |