|
| Status |
Public on Sep 18, 2024 |
| Title |
mouse kidney_sham_24h_3 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
genotype: WT
treatment: sham
|
| Treatment protocol |
In order to induce RIAKI, drinking water was withheld for 19 hours, followed by IM injection of either 50% glycerol (0.05 ml per 10 g body weight; N= 10) or saline (sham controls; N= 10) into the left hind limb under isoflurane anesthesia. For pain management, Rimadyl© (5 mg/kg body weight i.p.) was administered at 0 h and 3 h. At 24 h, blood was obtained from the mandibular venous plexus. Mice were euthanized by cervical dislocation, and kidneys were snap frozen or immersion-fixed in 4 % paraformaldehyde for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from frozen kidney samples was performed using RNA-STAT-60 (Tel-Test, Inc. USA) according to the manufacturer's instructions followed by cDNA synthesis with random primers and Superscript II reverse transcriptase (Thermo Fisher Scientific Inc., USA).
QIAseq UPX 3’ Transcriptome Kit (QIAGEN) according to the manufacturers instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
C56
|
| Data processing |
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.). The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 20.0.4 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. The reads were then mapped to the mMouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 mRNA annotation.
Assembly: GRCm38 v. 80
Supplementary files format and content: xlsx file, includes counts
|
| |
|
| Submission date |
Apr 23, 2024 |
| Last update date |
Sep 18, 2024 |
| Contact name |
Robert Labes |
| E-mail(s) |
robert.labes@charite.de
|
| Organization name |
Charité - Universitätsmedizin Berlin
|
| Department |
Institute of Translational Physiology
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE264651 |
Transcriptomic analysis of rhabdomyolysis induced kidney injury |
|
| Relations |
| BioSample |
SAMN41059478 |
| SRA |
SRX24344731 |
