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| Status |
Public on Dec 30, 2016 |
| Title |
Hippocampus_High-CPF_smRNA4 |
| Sample type |
SRA |
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| Source name |
Hippocampus_10 mg/kg/day CPF
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long Evans
gender: male
age: 14 wk
administered with: 10 mg/kg b.w./day chlorpyrifos (CPF) for 21 days
tissue: Hippocampus
molecule subtype: small RNA
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| 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 0 - 20), approximately 24 h apart. Fear conditioning testing was conducted for cohort A animals on the study day 20. Cohort B animals were not subjected to behavioral assessments. Fear conditioning training was given to the animals on day 19, approximately 24 h prior to contextual and cued memory assessments. A freezing response was used as a measure of cue and context-based learning.
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| 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.
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| Extracted molecule |
total 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.
Small RNA libraries were constructed using the TruSeq small RNA library preparation kit (Illumina, San Diego, CA) according to the manufacturer’s recommended protocol. 1 ug of total RNA were ligated to 3’ and 5’ adaptors containing bases targeting small RNAs and sequencing primer sequences, respectively. The enrichment of adaptor-ligated small RNA molecules was achieved by reverse transcription followed by limited-cycle polymerase chain reaction. Sample-specific barcode tags were incorporated into the small RNA libraries during the PCR process. The quality and concentration of newly constructed libraries were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Small RNA libraries constructed from the same type of tissue were pooled together in equimolar amounts and separated on 6% Novex Tris-Borate-EDTA gels (Life Technologies, Grand Island, NY) for size selection. Gel-purified sequencing libraries were quantified using KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA). Small RNA sequencing libraries were sequenced on the Illumina HiScanSQ according to the manufacturer's protocols.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
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| Description |
SM306
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| Data processing |
Basecalling performed using CASAVA version 1.8.2
Adaptor sequences were trimmed from the reads using the Cutadapt v1.2 package. Adaptor-trimmed reads with Q-score >20 and a length of 16-24 bases were aligned to the rat genome build UCSC Baylor 3.4/rn4 (Nov 2004) using bowtie with parameters -p 4 -q -n 1 -l 15 -e 80 -m 5 --best --strata.
Aligned reads were mapped to miRBase seuqnces (release 19) using Partek Genomics Suite version 6.6. Reads were assigned to mature miRNA sequences using a modified E/M algorith in Partek Genomics Suite and reads per million mapped miRNA (RPM) were calculated for each miRNA feature.
Genome_build: rn4
Supplementary_files_format_and_content: Tab-delimited text files including RPM values for each sample.
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| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christine Baer |
| E-mail(s) |
christine.e.baer2.ctr@mail.mil
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| Organization name |
Excet, Inc. / USACEHR
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| Department |
Environmental Health Program
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| Street address |
568 Doughten Drive
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| City |
Ft. Detrick |
| State/province |
MD |
| ZIP/Postal code |
21702-5010 |
| Country |
USA |
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| Platform ID |
GPL17116 |
| Series (2) |
| GSE74727 |
Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [smallRNA-seq] |
| GSE74728 |
Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats |
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| Relations |
| BioSample |
SAMN04244318 |
| SRA |
SRX1420922 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1931288_SM306.txt.gz |
2.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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