 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 26, 2018 |
| Title |
Kidney_24M_Vehicle_4 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: 24 months
treatment: Vehicle
|
| Treatment protocol |
RAD001 (Novartis) was formulated as a custom made microemulsion pre-concentrate at 2 % (w/w) and diluted to a final concentration prior to dosing per os. Rats were treated with RAD001 diluted in water, supplemented with 0.25% methylcellulose. Microemulsion pre-concentrate (adequate to a dose) diluted in water with 0.25% methylcellulose served as a vehicle control. For RAD001 treatment, 22.5 m old rats received per os either a vehicle daily or RAD001 once a week (seven doses of RAD001 in total) and vehicle daily for the rest of the week for 6 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap frozen kidneys, livers and gastrocnemius muscles were ground in liquid nitrogen by mortar and pestle and total RNA was extracted from ~30 mg of tissue powder using miRNeasy Micro Kit (Qiagen, 217084). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies, USA) and the integrity validated by the OD260/OD280 absorption ratio (>1.8) and by RIN score (>8) using Agilent 2100 Bioanalyzer, RNA 6000 Nano LabChip kit and Agilent 2100 Expert Software (Agilent Technologies, Inc., Santa Clara, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The 76bp paired-end reads were mapped to rat genome rn5 using STAR 2.4.5a with default parameters.
A genome-wide transcription signal map was derived by counting reads coverage in 10 bp step after normalizing to 1 million total reads. Stranded information was used to separate counts from sense and antisense strand.
For gene annotation, we first clustered the Refseq transcripts based on the sharing of splicing sites to get a master set of gene loci representing all alternative isoforms.
Signal from sense-strand were averaged across the exonic regions for each gene locus to measure the transcription level. This measure is equivalent to the RPKM “reads per kilobase per million” in other RNAseq analyses.
Genome_build: rn5
|
| |
|
| Submission date |
Jan 09, 2018 |
| Last update date |
Jun 26, 2018 |
| Contact name |
Jun Shi |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis Institutes for Biomedical Research
|
| Street address |
181 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE108978 |
Short-term low-dose mTORC1 inhibition in aged rats counter-regulates age-related gene changes and blocks age-related kidney pathology |
|
| Relations |
| BioSample |
SAMN08334890 |
| SRA |
SRX3545900 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2918192_rn5.Kidney_24M_Vehicle_4.bw |
106.7 Mb |
(ftp)(http) |
BW |
| GSM2918192_rn5.Kidney_24M_Vehicle_4.txt.gz |
411.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
