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Status |
Public on Aug 05, 2023 |
Title |
CT9w, Control-1 |
Sample type |
SRA |
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Source name |
kidney
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Organism |
Mus musculus |
Characteristics |
tissue: kidney treatment: Untreated
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Extracted molecule |
nuclear RNA |
Extraction protocol |
kidney samples of cortex with outer medulla were cut into <8mm3 pieces and homogenized in 2 ml of ice-cold Nuclei EZ Lysis buffer (NUC101; Sigma) with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615, Promega; AM2696, Life Technologies) using a Dounce homogenizer (885302-0002; Kimble Chase). The homogenate was further incubated on ice for 5 min with an additional 2 ml of lysis buffer. Then the homogenate was filtered through a 40-μm cell strainer (43-50040-51; pluriSelect) followed by centrifugation at 500 × g for 5 min at 4°C. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for another 5 min. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1x PBS, 1% bovine serum albumin, 0.1% RNase inhibitor) and filtered through a 5-μm cell strainer (43-50005; pluriSelect). Nuclei were processed using Chromium Single Cell Controller and Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, 3,000-4,000 nuclei were loaded onto the Chromium Controller to generate single cell GEMs coated with unique 10x cell barcodes, unique molecular identifiers (UMI), and poly dT oligos. RNA molecules from single nuclei were reverse-transcribed within droplets to generate barcoded cDNAs. After break emulsion, cDNA molecules were pre-amplified, fragmented, ligated to an adaptor, and amplified with sample indices, followed by a double-sided size selection using SPRI beads (Beckman Coulter). The final libraries were assessed by Bioanalyzer 2100 (Agilent) and Qubit HS DNA (ThermoFisher) and pooled.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
PT Features(Cis9w vs CT9w)-1sta.cvs
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Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 5.0.1 Assembly: mm10 Supplementary files format and content: Comma Separated Values (CSV)file and matrix files
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Submission date |
Aug 01, 2023 |
Last update date |
Aug 05, 2023 |
Contact name |
Zhengwei Ma |
E-mail(s) |
zma@augusta.edu
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Organization name |
Augusta University
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Street address |
1460 Laney walker Blvd.
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City |
Augusta |
State/province |
GA |
ZIP/Postal code |
30912 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE239749 |
Single-nucleus transcriptional profiling of chronic kidney disease after cisplatin nephrotoxicity |
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Relations |
BioSample |
SAMN36780578 |
SRA |
SRX21206123 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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