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| Status |
Public on Aug 10, 2016 |
| Title |
301 Heart 24 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Rattus norvegicus |
| Characteristics |
treatment: Heat
tissue: Heart
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| Treatment protocol |
We placed rats in the heat-stress arm of the experiment into a floor-standing incubator set at room temperature (22°C) 24 hours prior to initiation of heat stress experiments. Rats in the control arm were never introduced to the incubator environment and were kept at a normal housing temperature. Once Tc ≤ 37.3°C was measured the rats were returned to their original cages for the remainder of the experiment. Rats in the heat-stress arm were heated in the incubator at 37.0 ± 0.2°C until reaching a Tc of 41.8°C (Tc,Max). The remaining rats were placed in a new cage at the ambient housing temperature (22.0 ± 0.2°C) and euthanized at 24 hours or 48 hours. Time-matched controls were euthanized at times corresponding to Tc,Max, 24 hours, and 48 hours in the heat-stress arm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissues (heart, lung, liver, and kidney) stored at -80 °C in cryovials were placed on dry ice, cut into aliquots with a sterile scalpel on a pre-chilled titanium block, and placed in new tubes pre-chilled on dry ice. While working on dry ice, whole tissues (~25 mg) from the lung, liver, and kidney were cut from each sample and placed in 700 mL of QIAzol Lysis Reagent. Samples were homogenized with a TissueLyzer LT (Qiagen, Valencia, CA) for 5 min at 25 Hz twice, allowed to sit at room temperature for 5 min, and then placed at -80 °C. We homogenized heart tissue with a 6750 Freezer Mill with three sample microvials (Spex SamplePrep, Metuchen, NJ). RNA was isolated using the miRNeasy 96 kit according to the manufacturer’s instructions. The quality and quantity of RNA samples were evaluated with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using the Agilent RNA 6000 Nano Reagents and a multi-well Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
Small RNA libraries were constructed using the TruSeq small RNA library preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Adapter sequences were trimmed with Cutadapt software (version 2.6). In addition, low complexity sequences, such as homopolymer sequences, were removed with the Prinseq tool (version 0.20.4). To reduce the time required for sequence mapping, the redundant sequences in the file were collapsed with the FASTX collapse script obtained from the FASTX toolkit (version 0.0.13). The number of reads for each unique sequence were calculated and used in summarizing the mapping read count. The unique read sequences were then mapped against the reference rat miRNA sequence database from miRBase (Release 19) under the perfect match condition.
Genome_build: miRBase (Release 19)
Supplementary_files_format_and_content: The proccessed data contains normalized counts.
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| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Permenter |
| Organization name |
US Army Center for Environmental Health Research
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| Street address |
568 Doughten Dr
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| City |
Fort Detrick |
| State/province |
MD |
| ZIP/Postal code |
21758 |
| Country |
USA |
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| Platform ID |
GPL17116 |
| Series (1) |
| GSE81331 |
Alterations in Tissue microRNA after Heat Stress in the Conscious Rat: Potential Biomarkers of Organ-Specific Injury |
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| Relations |
| BioSample |
SAMN04979241 |
| SRA |
SRX1756643 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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