|
| Status |
Public on Mar 01, 2023 |
| Title |
A003_GEX |
| Sample type |
SRA |
| |
|
| Source name |
kidney and blood mixded
|
| Organism |
Homo sapiens |
| Characteristics |
tissue/cell type: kidney and blood mixded
disease: ANCA-GN
patient id: A003
|
| Growth protocol |
For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38-2020-A release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38-2020-A and mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (linked to the corresponding *_GEX sample records)
|
| |
|
| Submission date |
Apr 15, 2022 |
| Last update date |
Jun 27, 2024 |
| Contact name |
Yu Zhao |
| E-mail(s) |
yu.zhao@zmnh.uni-hamburg.de
|
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Department |
Institute of Medical Systems Biology
|
| Street address |
Falkenried 94
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE200880 |
GM-CSF drives immune-mediated glomerular disease by licensing monocyte-derived cells to produce MMP12 |
|
| Relations |
| Reanalyzed by |
GSE253633 |
| BioSample |
SAMN27597709 |
| SRA |
SRX14870288 |
