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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 17, 2024 |
| Title |
Patient 4 Urine 5' scRNAseq |
| Sample type |
SRA |
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| Source name |
Urine
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Urine
cell type: urine-derived cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Urine cells were spun down from urine at 500g for 5 mins and filtered through a 70 uM filter. Tumor cells were received freshly from the surgical operating room immersed in RPMI 1640 media (11875-093; Gibco). Tumors were immediately minced and digested using an enzume cocktail from a Tumor Dissociation Kit (130-095-929; Miltenyi Biotec) and mechanical disociation with heat using the 37C_h_TDK_2 program on the gentleMACS (130-096-427, Miltenyi Biotec). Cells were then filtered through 100 μm, 70 μm, and 40 μm cell filters. Whole peripheral blood was spun at 300g for 7 minutes, and plasma was removed and frozen down. PBMCs were isolated by centrifugation over a Ficoll400 cell separation solution (17-1440-03; GE Healthcare) with red blood cells removed by ACK lysis buffer (A10492-01; Gibco).
Single-cell RNA sequencing was conducted on these samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3’ or 5’ gene expression (GEX) V3 kit (as indicated in the sample title). Gel-Bead in Emulsions (GEMs) were created on the sample chip in the Chromium controller, and barcoded cDNA was extracted by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing as per manufacturer’s protocols. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis.
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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
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| Data processing |
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v. 5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated value and matrix files
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| Submission date |
May 16, 2024 |
| Last update date |
May 17, 2024 |
| Contact name |
Michelle A Tran |
| E-mail(s) |
michellet987@gmail.com
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| Phone |
3106639583
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| Organization name |
Icahn School of Medicine
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| Street address |
1470 Madison Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE267718 |
Single cell RNA sequencing (scRNAseq) of urine-derived cells, peripheral blood mononuclear (PBMC), and tumor cells from bladder cancer patients. |
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| Relations |
| BioSample |
SAMN41427815 |
| SRA |
SRX24585605 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8273658_Patient4Urine_barcodes.tsv.gz |
25.8 Kb |
(ftp)(http) |
TSV |
| GSM8273658_Patient4Urine_genes.tsv.gz |
287.6 Kb |
(ftp)(http) |
TSV |
| GSM8273658_Patient4Urine_matrix.mtx.gz |
26.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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