|
| Status |
Public on Jun 01, 2016 |
| Title |
Urine_Cisplatin_D4_1 |
| Sample type |
SRA |
| |
|
| Source name |
Genitourinary:Bladder:Urine
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Urine
strain: Sprague-Dawley
treatment: Cisplatin
dosage: 1500 mg/kg
regimen: IV; once
time point: D4
prep type: Qiagen RNeasy_96
Sex: Male
age: 9
age unit: Weeks
|
| Treatment protocol |
Eight rats each received one of the following: (1) a 5 ml intravenous administration of 2 or 5 mg/kg cisplatin or vehicle (0.9% sterile saline); (2) a 10 ml oral gavage of 400 or 1250 mg/kg APAP or vehicle (0.5% methylcellulose); or (3) a 10 ml oral gavage of 250 or 1500 mg/kg CCL4 or vehicle (corn oil). Cisplatin was purchased from Teva Pharmaceuticals while both APAP and CCL4 were purchased from Sigma-Aldrich. Four animals from each group were euthanized 24 hours post dose and the remaining four animals were euthanized at 72 hours post dose. Animals first received intramuscular injection of an anesthetic cocktail (ketamine HCl [75 mg/kg], xylazine [2.5 mg/kg] and acepromazine [2.5 mg/kg]) and exsanguinations were performed in accordance with accepted American Veterinary Medical Association guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from plasma or urine by Asuragen following a proprietary small-scale biofluid RNA isolation procedure. Samples were eluted in 20 μL of water to 10 urine equivalents (UE) or plasma equivalents (PE) per μL
Isolation of miRNA from 50 μ tissue samples used a lysis buffer (RLT [Qiagen] + 1% β mercaptoethanol) and a rotor-stator homogenizer
A TruSeq Small RNA Library Kit (Illumina) was used for library construction of rat miRNA
Sequencing was performed on the GAIIx (Illumina) at 36 base pair read length and targeting 12 million reads per sample
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
D1797001641
|
| Data processing |
OSA v4 (http://omicsoft.com/osa) was used to align the reads to the rat genome (Rnor_5.0) and to MiRBase (v.21) [44] allowing for two mismatches and excluding any reads that aligned to greater than 10 genomic locations
Expression levels were quantified by counting the number of reads aligned to mature miRNA region
Genome_build: rat genome (Rnor_5.0)
Supplementary_files_format_and_content: excel file includes miRNA count data for each sample
|
| |
|
| Submission date |
Mar 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pooja Shah |
| E-mail(s) |
pooja.shah@takeda.com
|
| Organization name |
Takeda Pharmaceuticals
|
| Street address |
40 Landsdowne Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL10669 |
| Series (1) |
| GSE79017 |
MicroRNA-SEQ analysis of kidney and liver damage in rat |
|
| Relations |
| SRA |
SRX1620301 |
| BioSample |
SAMN04539715 |
