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.
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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. |
Molecule Type: | polyA(+) RNA |
Library Source: | |
Library Layout: | SINGLE |
Library Strand: | Reverse |
Platform: | ILLUMINA |
Instrument Model: | Illumina NextSeq 500 |
Strand-Specific: | Specific |
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 |
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