|
| Status |
Public on May 27, 2022 |
| Title |
KO-P2: PBS-treated KO 2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole kidney
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Vehicle
genotype: Renal tubule BMAL1 KO
tissue: Whole kidney
|
| Treatment protocol |
One week after the end of DOX treatment, Type I diabetes was induced by intraperitoneal injections of streptozotocin (STZ, 50 mg/kg BW, daily for 5 days). Vehicle-treated mice received vehicle injections of PBS. All experiments were performed 8 weeks after the last STZ or vehicle injection.
|
| Growth protocol |
Animals were maintained ad libitum on the standard laboratory chow diet (KLIBA NAFAG diet 3800). Inactivation of the Bmal1 gene was induced by 2-week treatment with DOX (2 mg/ml in drinking water) of 8-week old Bmal1 lox/lox /Pax8-rtTA/LC1 mice (cKOt mice). Their littermate controls (Bmal1lox/lox mice) received the same DOX treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue acollection was performed from mice sacrificed at ZT9 (ZT – Zeitgeber time units; ZT0 is the time of light on and ZT12 is the time of light off). RNA from whole kidneys was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Genome_build: Mus musculus.GRCm38.92
Supplementary_files_format_and_content: raw gene counts for every gene in every sample
|
| |
|
| Submission date |
Jun 16, 2021 |
| Last update date |
May 27, 2022 |
| Contact name |
Sylvain Pradervand |
| E-mail(s) |
Sylvain.Pradervand@unil.ch
|
| Phone |
+41 21 692 39 08
|
| Organization name |
UNI Lausanne
|
| Department |
CIG
|
| Lab |
DNA Array Facility
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE178319 |
Dysfunction of the circadian clock in the renal tubule leads to enhanced renal gluconeogenesis and exacerbated hyperglycemia in diabetes |
|
| Relations |
| BioSample |
SAMN19729903 |
| SRA |
SRX11157871 |
