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| Status |
Public on Nov 15, 2024 |
| Title |
whole kidney snRNA seq of mouse #4442 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were extracted from flash frozen whole kidney samples. The specimens were thawed and minced thoroughly for one minute in NP40 lysis buffer (0.1% NP40, 10 mM Tris pH 7.5, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, and 40 U/mL RNAse inhibitor). Next, the suspension was further homogenized in 1 mL lysis buffer using a Dounce homogenizer (Kimble) with 20 strokes each using pestle A and pestle B. Subsequently, 4 mL of wash buffer (10 mM Tris, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 1% BSA [7.5% Fraction V], and 40 U/mL RNAse inhibitor) was added, filtered through a 30 µm strainer (Milteni), and centrifuged for 10 min at 200×g at 4 °C. The supernatant with debris was carefully removed using a glass Pasteur pipette and house vacuum, and the pellet was then resuspended in 5 mL wash buffer, filtered through a 5 µm strainer (Pluriselect), and centrifuged again. Nuclei were submitted to the Advanced Genomics Core at the University of Michigan for single-nucleus RNA sequencing using the 10X Genomics Chromium platform, following manufacturer instructions.
cDNA libraries were prepared using the Chromium platform following manufacturer instructions (10X Genomics).
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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 |
Processed data files include archived (.tar) versions of the filtered_feature_bc_matrix and raw_feature_bc_matrix folders generated by CellRanger (each of which contains the files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
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| Data processing |
Demultiplexing, barcode processing, gene counting, and aggregation were performed using CellRanger (10X Genomics, version cellranger-6.1.2).
Assembly: mm10 with EGFP, Cre, and tdTomato
Supplementary files format and content: Processed data files include archived (.tar) versions of the filtered_feature_bc_matrix and raw_feature_bc_matrix folders generated by CellRanger (each of which contains the files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
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| Submission date |
Sep 27, 2024 |
| Last update date |
Nov 15, 2024 |
| Contact name |
Jeffrey A Beamish |
| E-mail(s) |
jebeamis@med.umich.edu
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| Organization name |
University of Michigan
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| Department |
Department of Internal Medicine, Division of Nephrology
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| Street address |
1500 E. Medical Center Drive, SPC 5364
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE278289 |
Single nucleus RNA sequencing of mosiac Pax2 and Pax8 mutant proximal tubules |
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| Relations |
| BioSample |
SAMN43962319 |
| SRA |
SRX26221996 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8543510_sample_B_filtered_feature_bc_matrix.tar.gz |
114.1 Mb |
(ftp)(http) |
TAR |
| GSM8543510_sample_B_raw_feature_bc_matrix.tar.gz |
251.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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