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| Status |
Public on Mar 31, 2024 |
| Title |
W2, Visium |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
cell type: mesenchymal stem cells
genotype: B6
treatment: AAN CKD
time: Week 2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Freshly collected immune cells were isolated from human kidneys. Cross sections of kidney were digested in the commercially available collagenase, Liberase, for 30 minutes at 37 degrees Celsius. Red blood cells were lysed and the samples were resuspended in PBS. Samples were stained for Viability and resuspended in FACS Buffer (PBS, 5% FBS, 5% EDTA) and stained with CD45-FITC antibody. Samples were identified as being FITC positive using FACS (Aria, BD) and unstained samples were used as a negative control.
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 Cell Ranger software v6.0, samples were analyzed using Seurat v4.3.0. Kidney resident macrophages were identified via expression of C1qa, CD4 T cells were identified by Cd3e and Cd4
Unhashed, W2_m1_CD45 hashed with Biolegend B301 Cat 155831, W2_m2_CD45 hashed with Biolegend B305,Cat 155839
Raw files in W2_m1_CD45 contain the fastq files for both W2_m1 and W2_m2. They can be separated with the hashing antibodies listed above
Assembly: mm10
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| Submission date |
Mar 29, 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 |
GPL24247 |
| Series (1) |
| GSE228516 |
Aristolochic Acid Nephropathy 2 week time point of CD45+ cells |
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| Relations |
| BioSample |
SAMN33973738 |
| SRA |
SRX19812247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7123312_W2_spatial_aligned_fiducials.jpg.gz |
1.3 Mb |
(ftp)(http) |
JPG |
| GSM7123312_W2_spatial_detected_tissue_image.jpg.gz |
1.8 Mb |
(ftp)(http) |
JPG |
| GSM7123312_W2_spatial_scalefactors_json.json.gz |
177 b |
(ftp)(http) |
JSON |
| GSM7123312_W2_spatial_tissue_hires_image.png.gz |
9.7 Mb |
(ftp)(http) |
PNG |
| GSM7123312_W2_spatial_tissue_lowres_image.png.gz |
852.1 Kb |
(ftp)(http) |
PNG |
| GSM7123312_W2_spatial_tissue_positions_list.csv.gz |
57.2 Kb |
(ftp)(http) |
CSV |
| GSM7123312_w2_spatial_filtered_feature_bc_matrix.h5 |
14.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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