Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA731518: RNAseq analysis of PS+ vs PS- non-naive CD8 T cells sorted from peripheral blood of COVID-19 patients

Source: NCBI / GSE174786
Submission Date: May 20 2021
Release Date:
Update Date: Dec 08 2021

Summary: We report the transcriptional profile of phosphatidylserine (PS) positive and PS negative non-naive peripheral blood CD8 T cells from patients infected with SARS-CoV-2. PS+ CD8 T cells showed increased expression of cell cyclce and cell division associated genes and reduced expression of genes regulating translational initiation, when compared to PS- CD 8 T cells. Furthermore, PS+ CD8 T cells show increased expression of effector T cell genes.

Overall Design: non-naive (CCR7+CD45RA-, CCR7-CD45RA-, CCR7-CD45RA+) PS+ and PS- peripheral blood CD8 T cells were sorted from 4 COVID-19 patients and analysed by RNAseq WHOmax: the maximal COVID-19 disease severity score of the patient, classified using the World Health Organization's (WHO) eight-point ordinal scale for COVID-19 trial endpoints.

GEN Datasets:
GEND000469
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Peripheral blood was collected into lithium heparin tubes (Sarstedt). PBMCs were isolated by Biocoll density gradient (Merck) centrifugation and then directly stained for FACS sorting. Live, Dump-, C8+,CCR7+CD45RA-, CCR7-CD45RA-, CCR7-CD45RA+, PS+ and PS- were directly sorted into TRIZOL on a FACSAriaFusion (BD) using a 100 μm nozzle. Total RNA was isolated and purified using Monarch columns (NEB). Poly(A)+ RNA was isolated from the total RNA sample. First-strand cDNA synthesis was primed with a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. In this way, a strand specific PCR amplification of the cDNA was achieved using a proof-reading enzyme. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 250-700 bp was eluted from a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA size range was 250-700 bp. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 1x75 bp read length.
Library Construction Protocol: First-strand cDNA synthesis was primed with a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. In this way, a strand specific PCR amplification of the cDNA was achieved using a proof-reading enzyme. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 250-700 bp was eluted from a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA size range was 250-700 bp. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 1x75 bp read length.
Sequencing
Molecule Type: polyA(+) RNA
Library Source:
Library Layout: SINGLE
Library Strand: Reverse
Platform: ILLUMINA
Instrument Model: Illumina NextSeq 500
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
A Whole Virion Vaccine for COVID-19 Produced via a Novel Inactivation Method and Preliminary Demonstration of Efficacy in an Animal Challenge Model.
Vaccines . 2021-04-01 [PMID: 33916180]