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| Status |
Public on Jun 25, 2024 |
| Title |
Control 03, Kidney |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
cell type: FACS-sorted CD3+ cells
tissue: Kidney
treatment: None
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspensions were obtained from human kidney biopsies by enzymatic digestion in RPMI 1640 medium with collagenase D at 0.4 mg/ml (Roche, 11088858001) and deoxyribonuclease I (DNase I; 10 μg/ml; Sigma-Aldrich, 10104159001) at 37°C for 30 min followed by dissociation with gentle MACS (Miltenyi Biotec). Leukocytes from blood samples were separated using Leucosep tubes (Greiner Bio-One, 10349081). Cells were stained with fluorochrome-conjugated antibodies from BioLegend and BD Biosciences, CD45 BV510 (HI30), CD3 BV785 (OKT3), CD4 BV650 (RPA-T4), CD8 APC-R700 (RPA-T8), CXCR3 Pe/Dazzle (G025H7), CCR6 PerCP-Cy5-5 (G034E3). Cells were also stained with a dead cell stain (Molecular Probes, L10119) to exclude dead cells from analysis. FACS was performed on a FACSAria Fusion cell sorter (BD Biosciences). ScRNA-seq of human samples from the kidney and peripheral blood was performed from FACS-sorted CD3 positive T cells using Single Cell 3' v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina HiSeq4000.
libaries were constructed according to manufacturer specifications
Libraries were sequenced aiming at 50,000 reads per cell on an Illumina HiSeq4000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Single Cell 3' v2 (10x Genomics)
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| Data processing |
The Cell Ranger software (Cellranger v2.1.0 and v2.2.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome hg19. All quality control and preprocessing steps were performed in Seurat and R.
Assembly: hg19
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : h5 files output from CellRanger
Supplementary files format and content: .rds : Seurat Files created using the output from CellRanger
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| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Christian Krebs |
| E-mail(s) |
c.krebs@uke.de
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| Organization name |
UKE
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| Street address |
Martinistraße 52
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| City |
Hamburg |
| State/province |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE270533 |
Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease |
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| Relations |
| BioSample |
SAMN42010787 |
| SRA |
SRX25026968 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8346290_C03K.rds.gz |
305.2 Mb |
(ftp)(http) |
RDS |
| GSM8346290_C03K_filtered_gene_bc_matrices_h5.h5 |
5.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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