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| Status |
Public on Jul 18, 2024 |
| Title |
Gene expression profile at bulk (24h, 48h & 72h) and single nucleus (24h) level of mouse right kidney post sham operation and unilateral nephrectomy. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The mechanism driving the remarkable ability of the remaining kidney to enlarge and increase its function following removal of its contralateral pair remains elusive. To explore the pathways driving compensatory renal hypertrophy, comprehensive RNA-seq transcriptional studies in the kidneys of mice undergoing hypertrophy 24, 48 and 72 hours following nephrectomy have been undertaken and compared with mice undergoing sham operations. The results reveal substantial time dependent enhancement of cholesterol biosynthesis pathways, increases in mitochondrial gene expression and cell cycle perturbations. Single nuclei RNA-Seq 24 hours post nephrectomy was used to further explore cholesterol biosynthesis signature and its driver SREBP2. In a cell specific manner, snRNA-seq demonstrated that SREBP2 activity increases in proximal tubules and medullary thick ascending limb and is responsible for cell size regulation following IGF-1 stimulation. These results suggest a previously undescribed role for SREBP2 in the mechanism underlying compensatory renal hypertrophy. This mechanism might be amenable to therapeutic manipulation to enhance kidney size and function.
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| Overall design |
Mice were anaesthetised using 1.5-2.5% isoflurane/oxygen (1.5L/min), the left kidney was accessed with a mid-lateral skin incision and exposed. Adherent fat and the adrenal gland were bluntly dissected from the cranial pole. Renal blood supply was clamped and doubly ligated (Prolene 4-0). The clamp was removed, and the abdominal wall was closed by simple interrupted stitches (Prolene 4-0). Skin was closed with wound clips. Mice were given subcutaneous 0.5ml 0.9% sterile saline and Buprenorphine (0.05mg/kg) at time of surgery. Pain relief was given every 8-12h post-surgery as required for the first 24h. Sham operations were performed similarly without kidney removal. For bulk RNA-sequencing, RNA was extracted and quantified. Library preparation was performed using the Illumina TruSeq Stranded mRNA library preparation kit and sequenced using the NovaSeq system (Illumina) platform with 150bp paired end read length. For single nuclei RNA-sequencing, a small mid cross-section of the kidney was excised and processed for nuclei isolation using the EZ Nuclei Isolation Kit (Sigma-Aldrich) following the manufacturer's protocol. DAPI stained nuclei were isolated using FACS Aria Fusion (Becton Dickinson). The single nuclei suspension was then immediately loaded onto a Chromium Controller (10x Genomics) for single nuclei encapsulation, barcoding, and library preparation using the Chromium Single Cell 3' Reagent Kit v3 (10x Genomics) following the manufacturer's instructions. The prepared libraries were sequenced on an MGI FCL sequencer with 100bp paired end read length.
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| Contributor(s) |
Gleadle JM, Rojas-Canales D, Wong SW, Tucker EJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 18, 2023 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Jonathan Gleadle |
| E-mail(s) |
jonathan.gleadle@flinders.edu.au
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| Organization name |
Flinders University
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| Department |
College of Medicine and Public Health
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| Lab |
Renal lab
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| Street address |
3D226 Renal Lab, Flinders Medical Centre, Flinders Drive
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| City |
Bedford Park |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL28457 |
DNBSEQ-G400 (Mus musculus) |
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| Samples (40)
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| GSM7719505 |
Right kidney, Sham operated, 24h, rep1, RNAseq |
| GSM7719506 |
Right kidney, Sham operated, 24h, rep2, RNAseq |
| GSM7719507 |
Right kidney, Sham operated, 24h, rep3, RNAseq |
| GSM7719508 |
Right kidney, Sham operated, 24h, rep4, RNAseq |
| GSM7719509 |
Right kidney, Sham operated, 24h, rep5, RNAseq |
| GSM7719510 |
Right kidney, Sham operated, 24h, rep6, RNAseq |
| GSM7719511 |
Right kidney, Sham operated, 48h, rep1, RNAseq |
| GSM7719512 |
Right kidney, Sham operated, 48h, rep2, RNAseq |
| GSM7719513 |
Right kidney, Sham operated, 48h, rep3, RNAseq |
| GSM7719514 |
Right kidney, Sham operated, 48h, rep4, RNAseq |
| GSM7719515 |
Right kidney, Sham operated, 48h, rep5, RNAseq |
| GSM7719516 |
Right kidney, Sham operated, 48h, rep6, RNAseq |
| GSM7719517 |
Right kidney, Sham operated, 72h, rep1, RNAseq |
| GSM7719518 |
Right kidney, Sham operated, 72h, rep2, RNAseq |
| GSM7719519 |
Right kidney, Sham operated, 72h, rep3, RNAseq |
| GSM7719520 |
Right kidney, Sham operated, 72h, rep4, RNAseq |
| GSM7719521 |
Right kidney, Sham operated, 72h, rep5, RNAseq |
| GSM7719522 |
Right kidney, Sham operated, 72h, rep6, RNAseq |
| GSM7719523 |
Right kidney, Unilateral nephrectomised, 24h, rep1, RNAseq |
| GSM7719524 |
Right kidney, Unilateral nephrectomised, 24h, rep2, RNAseq |
| GSM7719525 |
Right kidney, Unilateral nephrectomised, 24h, rep3, RNAseq |
| GSM7719526 |
Right kidney, Unilateral nephrectomised, 24h, rep4, RNAseq |
| GSM7719527 |
Right kidney, Unilateral nephrectomised, 24h, rep5, RNAseq |
| GSM7719528 |
Right kidney, Unilateral nephrectomised, 24h, rep6, RNAseq |
| GSM7719529 |
Right kidney, Unilateral nephrectomised, 48h, rep1, RNAseq |
| GSM7719530 |
Right kidney, Unilateral nephrectomised, 48h, rep2, RNAseq |
| GSM7719531 |
Right kidney, Unilateral nephrectomised, 48h, rep3, RNAseq |
| GSM7719532 |
Right kidney, Unilateral nephrectomised, 48h, rep4, RNAseq |
| GSM7719533 |
Right kidney, Unilateral nephrectomised, 48h, rep5, RNAseq |
| GSM7719534 |
Right kidney, Unilateral nephrectomised, 48h, rep6, RNAseq |
| GSM7719535 |
Right kidney, Unilateral nephrectomised, 72h, rep1, RNAseq |
| GSM7719536 |
Right kidney, Unilateral nephrectomised, 72h, rep2, RNAseq |
| GSM7719537 |
Right kidney, Unilateral nephrectomised, 72h, rep3, RNAseq |
| GSM7719538 |
Right kidney, Unilateral nephrectomised, 72h, rep4, RNAseq |
| GSM7719539 |
Right kidney, Unilateral nephrectomised, 72h, rep5, RNAseq |
| GSM7719540 |
Right kidney, Unilateral nephrectomised, 72h, rep6, RNAseq |
| GSM7719541 |
Right kidney, Sham operated, 24h, rep1, snRNAseq |
| GSM7719542 |
Right kidney, Sham operated, 24h, rep2, snRNAseq |
| GSM7719543 |
Right kidney, Unilateral nephrectomised, 24h, rep1, snRNAseq |
| GSM7719544 |
Right kidney, Unilateral nephrectomised, 24h, rep2, snRNAseq |
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| Relations |
| BioProject |
PRJNA1006732 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241213_bulk_counts.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSE241213_bulk_meta.data.csv.gz |
1.0 Kb |
(ftp)(http) |
CSV |
| GSE241213_sn_counts.csv.gz |
82.6 Mb |
(ftp)(http) |
CSV |
| GSE241213_sn_meta.data.csv.gz |
141.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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