|
| Status |
Public on Jan 01, 2024 |
| Title |
HBsAg high group PBMC5 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
disease state: chronic hepatitis B patient
cell type: peripheral blood mononuclear cells
group: HBsAg high group
treatment: nucleoside analogues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Single Cell 3’ v3 Reagent Kit, or 10x Genomics Single Cell 5’ v2 Reagent Kit
10X Genomics Single Cell 3’ v3 Reagent Kit, and 10x Genomics Single Cell 5’ v2 Reagent Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
To process raw files to count matrices, 10x Genomics Cell Ranger 6.1.2 with the human reference genome GRCh38 was used with default settings.
Cell Ranger-processed filtered feature matrices were analyzed using R version 4.2.2 and Seurat version 4.3.0.
Assembly: GRCh38-1.2.0
Supplementary files format and content: Processed files with output of the 10X cellranger pipeline (filtered_feature_bc_matrix, .tsv and .matrix files).
Supplementary files format and content: Seurat objects (RDS files) with R scripts (Rmd and html files).
Supplementary files format and content: Processed data files FNAs (Cell Ranger-processed filtered feature matrices)
Supplementary files format and content: Processed data files PBMCs (Cell Ranger-processed filtered feature matrices)
|
| |
|
| Submission date |
Nov 08, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Andre Boonstra |
| E-mail(s) |
p.a.boonstra@erasmusmc.nl
|
| Organization name |
Erasmus MC
|
| Department |
Dept. of Gastroenterology and Hepatology
|
| Street address |
Dr. Molewaterplein 40
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE247322 |
Association of HBsAg levels with differential gene expression in NK, CD8 T, and memory B cells in treated patients with chronic HBV |
|
| Relations |
| BioSample |
SAMN38165969 |
| SRA |
SRX22429677 |
