|
| Status |
Public on Aug 20, 2023 |
| Title |
48-7 [ssRNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
single-cell RNA-seq of human: adult male PBMC seven days post vaccination
|
| Organism |
Homo sapiens |
| Characteristics |
timepoint: seven days post vaccination
tissue: PBMC
cell type: B-cell
Sex: male
age: 85
ethnicity: Not Hispanic or Latino
race: White
library type: scRNA-seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 100x100 paired-end reads was used to sequence gene expression libraries.
ssRNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Gene expression analysis of CellRanger output was performed using Seurat v.3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv & features.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.
|
| |
|
| Submission date |
May 25, 2021 |
| Last update date |
May 10, 2024 |
| Contact name |
Steven Kleinstein |
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
Kleinstein
|
| Street address |
300 George St.
|
| City |
New Haven |
| State/province |
Ct |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE175522 |
High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell Gene Expression) |
| GSE175524 |
High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults |
|
| Relations |
| BioSample |
SAMN19189500 |
| SRA |
SRX10918773 |
