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| Status |
Public on Jun 01, 2021 |
| Title |
Sham Model |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Mus musculus |
| Characteristics |
disease: Reference
tissue source: Nephrectomy
storage: OCT at -80C
gender: Male
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| Treatment protocol |
n/a
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Human Kidney tissue was obtained from a deceased donor nephrectomy intended for transplant. It was frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
Murine Kidney tissue was obtained from a mice upon sacrifice and immediately frozen on OCT. 10 um of cross-sectional tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Expression counts determined by spaceranger 1.0.0 and reference genomes GRCh38-3.0.0 and mm10-3.0.0
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Genome_build: Hg38 and mm10
Supplementary_files_format_and_content: position and counts on csv files, images on tiff files.
Supplementary_files_format_and_content: Human_Nephrectomy.tar.gz - Spots position, filtered counts matrix, and images for the Human Nephrectomy, as outputted from SpaceRanger.
Supplementary_files_format_and_content: Sham_Model.tar.gz - Spots position, filtered counts matrix, and images for the Sham murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: IRI_Model.tar.gz - Spots position, filtered counts matrix, and images for the Ischemia Reperfusion Injury murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: CLP_Model.tar.gz - Spots position, filtered counts matrix, and images for the Cecal Ligation Puncture murine model, as outputted from SpaceRanger.
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| Submission date |
Apr 02, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Michael T Eadon |
| Organization name |
Indiana University
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| Street address |
950 W Walnut St
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE171406 |
Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury |
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| Relations |
| BioSample |
SAMN18605318 |
| SRA |
SRX10505829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5224979_B1.tif.gz |
152.7 Mb |
(ftp)(http) |
TIFF |
| GSM5224979_counts_B1_S2.csv.gz |
8.7 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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