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| Status |
Public on Jun 14, 2024 |
| Title |
CropSeq NTN, Sample 1 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
cell type: T cells
treatment: crescentic glomerulonephritis
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Kidneys were incubated at 37 °C for 40 min in RPMI 1640 Medium (Thermo Fisher) containing 10% heat inactivated FBS, 1% P/S, 0.4 µg/ml Collagenase D (Roche, Basel, Switzerland) and 0.2 µg/ml DNAse (Roche). Subsequently, tissue was dissociated using the GentleMACS Dissociator and C-Tubes (both Miltenyi Biotec) and leukocytes were isolated using a gradient centrifugation with 37 % Percoll (GE Healthcare). After the centrifugation, cells were washed with DPBS (Gibco). CD4+ T cells were enriched using the EasySep Mouse CD4+ T cell Isolation Kit according to manufacturer’s instructions (Stemcell Technologies, Vancouver, Canada). Enriched cells were sorted by Fluorescence-activated cell sorting (FACS) for CD4+ T cells, GFP signal and eBFP2 signal.
All steps were performed according to standard protocol of the Chromium Single Cell 3' v3 kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics scRNA-seq using Chromium Single Cell 3' v3
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| Data processing |
10x Genomics raw sequencing data were processed using CellRanger software (version 3.1, 10x Genomics, Pleasanton, CA).
Assembly: mm10
Supplementary files format and content: Cellranger output: Tab seperated values files and Matrix table with raw gene counts
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| Submission date |
May 17, 2024 |
| Last update date |
Jun 14, 2024 |
| Contact name |
Malte Hellmig |
| Organization name |
University Medical Center Hamburg-Eppendorf
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| Department |
III. Department of Medicine
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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 |
GPL24247 |
| Series (1) |
| GSE267740 |
Targeting T cell plasticity in kidney and gut inflammation by pooled single-cell CRISPR screening |
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| Relations |
| BioSample |
SAMN41434335 |
| SRA |
SRX24589485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8274943_NTN_1_19_5_barcodes.tsv.gz |
50.7 Kb |
(ftp)(http) |
TSV |
| GSM8274943_NTN_1_19_5_features.tsv.gz |
227.9 Kb |
(ftp)(http) |
TSV |
| GSM8274943_NTN_1_19_5_matrix.mtx.gz |
71.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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