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Sample GSM7140131 Query DataSets for GSM7140131
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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