 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 04, 2024 |
| Title |
VCOV_s03_P0,γδ scTCR-seq |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: PBMC
age: 25-50 years old
gender: Male
treatment: P0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats of HDs (n=6) or from 6 healthy vaccinated subjects through Lympholyte®-H Cell Separation density gradient solution (Cedarlane Laboratories, Burlington, North Carolina, USA) according to the manufacturer’s instruction. In vitro experiments were performed on freshly isolated PBMCs, with a viability greater than 95%, while single-cell ones on PBMCs previously frozen in Fetal Bovine Serum (FBS) supplemented with 10% of the cryoprotective Dimethyl Sulfoxide (DMSO).
Thawed PBMC samples were evaluated for viability prior to scRNA-seq analysis, and all were ≥95% viable. Cells were resuspended in a volume equivalent to 10,000 target cells for each sample, and were individually loaded onto a Chromium single-cell controller (10X Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were then lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Complementary DNAs (cDNA) were generated and split to generate γδ scTCR-seq libraries. To this end, gene-specific primers 25 were used within the 5′ regions of the TRGC and TRDC segments for the enrichment of TCR transcripts (v1.1 chemistry) Complementary DNAs were amplified, and the quality was assessed using an Agilent 4200 Tapestation. The scTCR-seq libraries were sequenced on Illumina NextSeq 550 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
10x Genomics
VCOV_s03_P0_filtered_contig_annotations.csv
Sample 11
|
| Data processing |
*library strategy: scTCR-seq
The γδ TCR alignment and consensus annotations were performed using Cell Ranger VDJ tools v3.1.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: Comma-separated values (csv) files
|
| |
|
| Submission date |
Mar 04, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Sara Terzoli |
| E-mail(s) |
sara.terzoli@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Street address |
Via Alessandro Manzoni, 56
|
| City |
Rozzano, Milan |
| ZIP/Postal code |
20089 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE260763 |
Expansion of memory Vδ2 T cells following SARS-CoV-2 vaccination revealed by temporal single-cell transcriptomics |
|
| Relations |
| BioSample |
SAMN40253114 |
| SRA |
SRX23828826 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8124002_VCOV_s03_P0_filtered_contig_annotations.csv.gz |
942.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
