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| Status |
Public on Mar 31, 2024 |
| Title |
D1 kidney, AKI, visium |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
gender: male
disease state: Acute Kidney Injury
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Human kidney sections were frozen in OCT. 10 micron sections were cut and processed according to the Visium platform protocol
RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression and Visium spatial transcriptomics kits
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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, barcoded processing, gene counting and aggregation were made using the Space Ranger software, samples were analyzed using Seurat v4.3.0.
Assembly: human GRCh38 (GCA_000001405.28)
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| Submission date |
Mar 24, 2023 |
| Last update date |
Mar 31, 2024 |
| Contact name |
James F George |
| E-mail(s) |
jfgeorge@uabmc.edu
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| Phone |
2059344261
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| Organization name |
University of Alabama at Birmingham
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| Street address |
1720 2nd Ave South
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| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
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| Relations |
| BioSample |
SAMN33905401 |
| SRA |
SRX19766574 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7115963_D1_barcodes.tsv.gz |
19.9 Kb |
(ftp)(http) |
TSV |
| GSM7115963_D1_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM7115963_D1_matrix.mtx.gz |
16.5 Mb |
(ftp)(http) |
MTX |
| GSM7115963_D1_spatial_aligned_fiducials.jpg.gz |
1.5 Mb |
(ftp)(http) |
JPG |
| GSM7115963_D1_spatial_detected_tissue_image.jpg.gz |
1.8 Mb |
(ftp)(http) |
JPG |
| GSM7115963_D1_spatial_scalefactors_json.json.gz |
177 b |
(ftp)(http) |
JSON |
| GSM7115963_D1_spatial_tissue_hires_image.png.gz |
10.9 Mb |
(ftp)(http) |
PNG |
| GSM7115963_D1_spatial_tissue_lowres_image.png.gz |
953.5 Kb |
(ftp)(http) |
PNG |
| GSM7115963_D1_spatial_tissue_positions_list.csv.gz |
57.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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