|
| Status |
Public on Jul 17, 2015 |
| Title |
Rat 12 Olanzapine 24h |
| Sample type |
SRA |
| |
|
| Source name |
gastrocnemius muscle
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Crl:SD
charlers river strain code: 400
body weight gms: 400
|
| Treatment protocol |
For the olanzapine group, the venous catheter was attached to a New Era Pump Systems syringe pump (Model NE-300) filled with olanzapine (Dr. Reddy’s Laboratories Ltd, Hyderabad, India) in sterile saline (infusion: 1mg/100g BW loading dose for 0.5h and then 0.04mg/100g/h continuously for 23.5h). Control rats were infused with vehicle at the same rate and volume.
|
| Growth protocol |
Male Sprague Dawley rats (150-175g) from Charles River Laboratories (Cambridge, MA, USA) were acclimated to single housing for several weeks while being maintained on a 12:12 h light dark cycle at ~21°C and provided free access to water and a standard rodent chow (2018, Harlan Laboratories, Madison, WI)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gastrocnemius was then surgically removed under isoflurane anesthesia (carried with 100% O2), and frozen between two aluminum blocks cooled to the temperature of liquid nitrogen and then stored at -80oC until RNA was isolated. Frozen muscle tissue was pulverized in liquid nitrogen using mortar and pestle, followed by bead mill homogenization (Bullet Blender, Next Advance) using stainless steel beads (Next Advance, cat# SSB14B) and mirVana RNA isolation kit (Life Technologies). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RIN was determined for each sample using Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies).
The cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Olanzapine IV infused 24 h
|
| Data processing |
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter trimmed fastq files were generated.
Merged fastq files from lane 1 and lane 2. Fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using Rnor_5.0 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1 using -u and -N option. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used Enemble (release 77) gtf file as guided annotation file.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: FPKM gene expression data
|
| |
|
| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuka Imamura Kawasawa |
| E-mail(s) |
yui102@psu.edu
|
| Organization name |
Penn State University
|
| Department |
College of Medicine, Pharmacology
|
| Street address |
500 University Dr.
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE65787 |
Evidence from mRNA-Sequencing that Acute Olanzapine Infusion is Initiating a Skeletal Muscle Fiber Type Transition In Rat Gastrocnemius |
|
| Relations |
| BioSample |
SAMN03338707 |
| SRA |
SRX871036 |
