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Sample GSM3823944 Query DataSets for GSM3823944
Status Public on Sep 10, 2019
Title Diabetes Sample 3 (snRNAseq)
Sample type SRA
Source name Human Diabetic Kidney
Organism Homo sapiens
Characteristics tissue: kidney
disease state: diabetic
age: 57
a1c: 9.7
gfr: 89
global glomerulosclerosis: Mild 10-25%
ifta: 1-10%
gender: F
Growth protocol ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 10e6 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).
Extracted molecule total RNA
Extraction protocol Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Samples were cut into <2-mm pieces and homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and then centrifuged at 500×g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1× PBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-μm cell strainer (43–50020–50; pluriSelect), and counted.
Libraries were prepared according to Illumina's instructions and accompanying 10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit
Single Nucleus RNA Sequencing (snRNAseq)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description snRNAseq
Data processing Count matrices were generated with zUMIs v2.0 and saved as .rds files
Seurat objects were created from the count matrices and filtered using min.cells=3 and low.thresholds=500 (Seurat v2.3.4)
Seurat objects from control and diabetic samples were combined using the RunMultiCCA function to generate combined.rds
Genome_build: GRCh38
Supplementary_files_format_and_content: individual rds files were generated from count matrices using zUMIs v2.0 and Seurat v2.3.4
Submission date May 29, 2019
Last update date Sep 10, 2019
Contact name Parker C Wilson
Organization name Washington University in St. Louis
Street address 660. S Euclid Ave., CB 8118
State/province MO
ZIP/Postal code 63110
Country USA
Platform ID GPL24676
Series (1)
GSE131882 The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy
BioSample SAMN11878523
SRA SRX5914370

Supplementary file Size Download File type/resource
GSM3823944_diabetes.s3.dgecounts.rds.gz 157.5 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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