|
| Status |
Public on Feb 02, 2021 |
| Title |
Spot_urine_patient1_visit2 |
| Sample type |
SRA |
| |
|
| Source name |
urine
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Diabetic Kidney Disease
subject id: patient1
tissue: urine
barcode prefix: S1155844
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All steps were performed on ice or at 4 degree Celsius. The urine volume was measured and the sample was transferred into a 50 ml conical tube and centrifuged at 1000 rpm for 5 minutes. The supernatant was carefully removed leaving about 1ml in the tube. Next, the cells were suspended in 1X D-PBS and centrifuged at 1000 rpm for 5 minutes. This process was repeated twice. The pelleted cells were suspended in 1 ml of 1X D-PBS and passed through a 40um cell strainer. After centrifugation at 1,000 RPM for 5 mins, cell pellet was resuspended in appropriate volume of 1X D-PBS (resuspension volume was approximated based on the pellet size). Cell number and viability were analyzed using Countess Auto Counter (Invitrogen, C10227).
cDNA libraries were prepared according to the manufacturer’s protocol (Single Cell 3’ Reagent Kits v3, 10x Genomics, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Spot samples refer to spot urine samples obtained from the sampling of a single untimed urine specimen, voided spontaneously by the patient.
|
| Data processing |
FASTQ files from each 10X single cell run were processed by Cell Ranger v3.0.2 (10X Geonmics).
Genome_build: Human genome reference GRCh38
Supplementary_files_format_and_content: Count matrix for all genes and all cells after quality control filtering
|
| |
|
| Submission date |
Sep 08, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Katalin Susztak |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Medicine
|
| Lab |
Susztak Lab
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE157640 |
Urinary single cell profiling captures cellular diversity of the kidney |
|
| Relations |
| BioSample |
SAMN16079407 |
| SRA |
SRX9090980 |
