|
| Status |
Public on Jul 28, 2022 |
| Title |
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Purpose: Single cell sequencing has advanced our understanding of kidney biology. The goals of this study are to compare single nucleus RNA (snRNA-seq) and single nucleus assay for transposase accessible chromatin sequencing (snATAC-seq) from healthy control donors and donors with type 2 diabetic kidney disease to identify altered signaling pathways and chromatin accessibility patterns observed in diabetic kidney disease.
Methods: Nuclear dissociation of human kidney cortex samples was performed on samples obtained from patients undergoing tumor nephrectromy or deceased organ donors. snRNA-seq and snATAC-seq libraries were prepared using 10X Genomics kits according to manufacturers instructions. For this study, two healthy control libraries from one donor were prepared with the following chemistries (1 - single cell 3-prime v3, 1 - single cell ATAC v1) and nine DKD libraries from seven donors were prepared with the following chemistries (2 - single cell 5-prime v2 paired-end, 7 - single cell ATAC v1).
Raw data for three healthy control and three DKD snRNA-seq libraries sequenced with single nucleus 5-prime R2 only can be found in GSE13188213. Raw data for two healthy control snRNA-seq sequenced with single nucleus 5-prime paired-end and five snATAC-seq single nucleus ATAC v1 libraries can be found in GSE151302. snRNA-seq and snATAC-seq libraries from these earlier studies were recounted with cellranger (v4.0) or cellranger-atac (v2.0) to provide consistency across processed data files.
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| |
|
| Overall design |
snRNA-seq and snATAC-seq of human kidney cortex from patients with and without type 2 diabetic kidney disease
|
| Web link |
https://github.com/p4rkerw/Wilson_Muto_NComm_2022
|
| |
|
| Contributor(s) |
Wilson PC, Muto Y, Humphreys BD |
| Citation(s) |
36068241 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| K08 DK126847 |
The Single Cell Landscape of Early Human Diabetic Nephropathy |
WASHINGTON UNIVERSITY |
Parker C. Wilson |
| P30 DK020579 |
Diabetes Research Center |
WASHINGTON UNIVERSITY |
Clay F. Semenkovich |
| R01 DK103740 |
Mechanisms of Successful vs. Failed Kidney Repair |
WASHINGTON UNIVERSITY |
BENJAMIN D. HUMPHREYS |
|
| Submission date |
Jan 26, 2022 |
| Last update date |
Oct 31, 2022 |
| Contact name |
Parker C Wilson |
| Organization name |
Washington University in St. Louis
|
| Street address |
660. S Euclid Ave., CB 8118
|
| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (11)
|
|
| Relations |
| BioProject |
PRJNA800746 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE195460_Control1_filtered_feature_bc_matrix.h5 |
24.0 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control1_filtered_peak_bc_matrix.h5 |
70.6 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control1_fragments.tsv.gz |
1.9 Gb |
(ftp)(http) |
TSV |
| GSE195460_Control1_fragments.tsv.gz.tbi.gz |
1.0 Mb |
(ftp)(http) |
TBI |
| GSE195460_Control2_filtered_feature_bc_matrix.h5 |
7.5 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control2_filtered_peak_bc_matrix.h5 |
56.8 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control2_fragments.tsv.gz |
1.5 Gb |
(ftp)(http) |
TSV |
| GSE195460_Control2_fragments.tsv.gz.tbi.gz |
901.6 Kb |
(ftp)(http) |
TBI |
| GSE195460_Control3_filtered_feature_bc_matrix.h5 |
16.6 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control3_filtered_peak_bc_matrix.h5 |
126.6 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control3_fragments.tsv.gz |
2.2 Gb |
(ftp)(http) |
TSV |
| GSE195460_Control3_fragments.tsv.gz.tbi.gz |
1.1 Mb |
(ftp)(http) |
TBI |
| GSE195460_Control4_filtered_feature_bc_matrix.h5 |
10.9 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control4_filtered_peak_bc_matrix.h5 |
78.9 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control4_fragments.tsv.gz |
1.3 Gb |
(ftp)(http) |
TSV |
| GSE195460_Control4_fragments.tsv.gz.tbi.gz |
832.6 Kb |
(ftp)(http) |
TBI |
| GSE195460_Control5_filtered_feature_bc_matrix.h5 |
8.8 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control5_filtered_peak_bc_matrix.h5 |
85.7 Mb |
(ftp)(http) |
H5 |
| GSE195460_Control5_fragments.tsv.gz |
1.3 Gb |
(ftp)(http) |
TSV |
| GSE195460_Control5_fragments.tsv.gz.tbi.gz |
833.2 Kb |
(ftp)(http) |
TBI |
| GSE195460_DN1_filtered_feature_bc_matrix.h5 |
16.5 Mb |
(ftp)(http) |
H5 |
| GSE195460_DN2_filtered_feature_bc_matrix.h5 |
9.4 Mb |
(ftp)(http) |
H5 |
| GSE195460_DN3_filtered_feature_bc_matrix.h5 |
9.6 Mb |
(ftp)(http) |
H5 |
| GSE195460_RAW.tar |
14.0 Gb |
(http)(custom) |
TAR (of H5, TBI, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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