|
| Status |
Public on Dec 30, 2016 |
| Title |
Hippocampus_Control_mRNA3 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus_vehicle control
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long Evans
gender: male
age: 14 wk
administered with: vehicle control (peanut oil) for 21 days
tissue: Hippocampus
|
| Treatment protocol |
Rats were 11 weeks old at the initiation of dosing, and individual body weights ranged from 350 g to 450 g. Two CPF formulations (3 or 10 mg/kg b.w./day) and the vehicle control (peanut oil) were administered by subcutaneous (s.c.) injection for 21 consecutive days (study days 1 - 20), approximately 24 h apart.
|
| Growth protocol |
All animals used in this study were housed and maintained in the animal facilities at WIL Research Laboratories, LLC (Ashland, OH) that are fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC International). Research was conducted in compliance with the Animal Welfare Act, and other Federal statutes and regulations relating to animals and experiments involving animals and adheres to principles stated in the Guide for the Care and Use of Laboratory Animals (National Research Council 2011). Nine-week old Long Evans (LE) male rats were received from Charles River Laboratories, Inc. (Raleigh, NC) and acclimated for at least ten days. The animals were housed individually in suspended stainless steel wire mesh cages in a humidity and temperature-controlled room (50% ± 20% and 25 °C) with a 12-hour (h) light/12-h dark cycle (lights on at 0600). Rats were provided ad libitum access to rodent chow (Certified Rodent LabDiet 5002, PMI Nutrition International, LLC, St. Louis, MO) and reverse-osmosis treated water throughout the study. Individual body weights were recorded twice weekly.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA including small non-coding RNA was isolated from the CA1 region of rat hippocampus using miRNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Thirteen rat hippocampus RNA samples were selected from a CPF treatment group (10 mg/kg b.w./day CPF, n=6) or a vehicle control group (n=7). Total RNAs were processed for RNA-seq using the TruSeq RNA sample prep kit v2 (Illumina, San Diego, CA) according to the manufacturer’s protocol (Illumina, San Diego, CA). The rat hippocampus RNA libraries were clustered onto a TruSeq V3 flowcell, and subjected to a 100-cycle single read run (1x100 cycles) on Illumina HiScanSQ sequencing instrument according to the protocols described by the manufacturer (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
R108
|
| Data processing |
Basecalling performed using CASAVA version 1.8.2
Pre-processed FASTQ reads were filtered based on sequence base quality scores (Q > 20) using the PRINSEQ package. Quality-filtered reads were trimmed for 50 bases from the 3' end; only the 50 bases from the 5' end were used for alignment. Trimmed reads were aligned to the rat genome RGSC Rnor_5.0/rn5 build (March 2012) using TopHat v2.0 with default parameters.
Read counts were normalized to the total number of reads per kilo-base of transcript per million mapped reads (RPKM) and summarized to the gene level using a modified E/M algorithm in Partek Genomics Suites v6.6
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample.
|
| |
|
| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christine Baer |
| E-mail(s) |
christine.e.baer2.ctr@mail.mil
|
| Organization name |
Excet, Inc. / USACEHR
|
| Department |
Environmental Health Program
|
| Street address |
568 Doughten Drive
|
| City |
Ft. Detrick |
| State/province |
MD |
| ZIP/Postal code |
21702-5010 |
| Country |
USA |
| |
|
| Platform ID |
GPL17116 |
| Series (2) |
| GSE74726 |
Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [RNA-seq] |
| GSE74728 |
Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats |
|
| Relations |
| BioSample |
SAMN04244321 |
| SRA |
SRX1420886 |
