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| Status |
Public on Jul 20, 2023 |
| Title |
NAc METH RNA rep4 |
| Sample type |
SRA |
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| Source name |
Nucleus accumbens
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: Nucleus accumbens
treatment: Methamphetamine
Stage: Adult
Sex: male
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| Treatment protocol |
(+ )-Methamphetamine hydrochloride (METH, 10 mg/kg) (Sigma-Aldrich, St. Louis, MO) or saline (1 mL/kg) was administered to the rats every 2 h in four successive intraperitoneal (i.p.) injections. To measure hyperthermia, the core body temperatures of the rats were measured with a rectal probe digital thermometer (Thermalert TH-8; Physitemp Instruments, Clifton, NJ) before the beginning of the treatment (baseline temperatures) and at 1 h after each METH or saline injection.
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| Growth protocol |
Adult male Sprague-Dawley rats (Harlan, Indianapolis, IN, USA) (weighing 250–300 g on arrival) were pair-housed under a 12 h light/dark cycle in a temperature-controlled (20–22 °C) and humidity-controlled room. Food and water were available ad libitum. The animals were allowed to acclimatize for one week before the start of the study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated via TRIzol Reagent (Thermo Fisher Scientific, 15596026), Phasemaker Tubes (Thermo Fisher Scientific, A33248) and RNA Clean & Concentrator-5 (Zymo Research, R1013).
RNA-seq libraries were then constructed using 10ng of rRNA depleted total RNA with Universal Plus mRNA-seq kit (TECAN, 0520-A01) following the kit manual.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA-seq data were processed by Cutadapt (v2.7; --quality-cutoff=15,10 --minimum-length=36), FastQC (v0.11.4), and to do the trimming and QC report
STAR (v2.5.2b; --quantMode TranscriptomeSAM --outWigType bedGraph --outWigNorm RPM) was used to do rat genome mapping
gene expressions in rat brain regions was calculated by featureCounts (-p -T 4 -Q 10) based on UCSC gene annotation of rat
Assembly: rn6
Supplementary files format and content: bedgraph format; bg.gz files for showing RNA-seq signals
Supplementary files format and content: reads count of genes generated by featureCount for every sample
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample
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| Submission date |
Mar 24, 2022 |
| Last update date |
Jul 20, 2023 |
| Contact name |
Benpeng Miao |
| Organization name |
Washington University in St. Louis
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| Department |
Developmental Biology
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| Lab |
Bo Zhang Lab
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| Street address |
4480 Clayton Avenue
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| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL20084 |
| Series (2) |
| GSE199363 |
Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain [RNA-seq] |
| GSE199374 |
Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain |
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| Relations |
| BioSample |
SAMN26933931 |
| SRA |
SRX14603791 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5971065_NAc_METH_RNA_rep4.bedGraph.gz |
320.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM5971065_NAc_METH_RNA_rep4.genes.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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