GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE168876 Query DataSets for GSE168876
Status Public on Sep 13, 2021
Title Spiny mice (Acomys cahirinus) activate unique transcriptional programs after severe kidney injuries and regenerate organ function without fibrosis
Organisms Acomys cahirinus; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goal of this study was to characterize the kidney transcriptome of Mus musculus and Acomys cahirinus after unilateral ureteral obstruction (UUO) kidney injury.
Methods: Kidney mRNA-seq profiles of 10 week old mouse and spiny mouse were generated at 2 day and 5 days after unilateral ureteral obstruction injury in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Salmon, edgeR and a limma-voom pipeline in R.
Results: For both Mus musculus and Acomys cahirinus kidneys, we mapped about 50 million sequence reads per sample to the mouse transcriptome and identified 20580 transcripts in kidneys of Mus musculus and 54075 transcripts in the kidneys of Acomys cahirinus. Using 1.5 fold change and FDR < 0.05, number of transcripts that are significantly different between Mus musculus samples: 3915 between normal and day 2 after UUO, 5365 between normal and day 5 after UUO. For Acomys cahirinus: 1765 between normal and day 2 after UUO, 2499 between normal and day 5 after UUO.
Conclusions: Our study demonstrate there were many conserved responses to kidney injury between M. musculus and A. cahirinus despite the divergent outcomes for kidney fibrosis.
Overall design Kidney mRNA profiles of 10 week old mouse and Spiny mouse 2 and 5 days after unilateral ureteral obstruction kidney injury.
Contributor(s) Okamura D, Majesky M
Citation(s) 34849462
Submission date Mar 14, 2021
Last update date Dec 21, 2021
Contact name Daryl Okamura
Organization name Seattle Children’s Research Institute
Department Center for Developmental Biology & Regenerative Medicine
Street address 1900 9th Ave
City Seattle
State/province Washington
ZIP/Postal code 98101
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL29848 Illumina NovaSeq 6000 (Acomys cahirinus)
Samples (18)
GSM5171802 Mus musculus sham rep1
GSM5171803 Mus musculus sham rep2
GSM5171804 Mus musculus sham rep3
BioProject PRJNA714406
SRA SRP310563

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE168876_Acomys_day_2_vs_acomys_sham.xlsx 132.5 Kb (ftp)(http) XLSX
GSE168876_Acomys_day_5_vs_acomys_sham.xlsx 180.3 Kb (ftp)(http) XLSX
GSE168876_Mouse_day_2_vs_mouse_sham.xlsx 296.7 Kb (ftp)(http) XLSX
GSE168876_Mouse_day_5_vs_mouse_sham.xlsx 404.3 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap