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| Status |
Public on Sep 03, 2020 |
| Title |
F1AO1 |
| Sample type |
SRA |
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| Source name |
Nucleus accumbens
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| Organism |
Rattus norvegicus |
| Characteristics |
age: post-natal day 14
strain: Sprague Dawley Rat
tissue: Nucleus accumbens
generation: F1
treatment: in utero oxycodone exposure
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| Treatment protocol |
For the in utero exposure animals (IUO), an ascending dosing procedure was used wherein doses of 10 mg/kg/day oxycodone (oxy) were orally gavaged for 5 days followed by 0.5 mg/kg/day escalation for 10 days to a final dose of 15 mg/kg/day, after which F0 females were mated with proven male breeders, and the treatment regimen continued throughout mating, gestation, and parturition until weaning. For post-natal exposure (PNO), F0 dams were orally gavaged with 15 mg/kg/day of oxy after parturition until weaning. F1 pups were randomly selected from the litters and bred with males to produce the F2 generation. F1 animals were not dosed with oxy prior to/post breeding; they were only exposed in utero or via the breastmilk.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Using a brain matrix, nucleus accumbens sections were removed from the P14 brains of each group from both generations. Tissues were frozen on dry ice. Total RNA was isolated from each sample using the Zymo Direct-Zol RNA kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Preparation of clean sequence reads: Constructed sequencing libraries were subject to sequencing with Illumina Novaseq 6000 platform (paired-end, 150 bp). Prior to assembly, reads containing sequencing adaptors, reads containing sequencing primers, and sequences with q quality score lower than 20 were removed.
Alignment of reads: The cleaned sequencing reads were aligned to reference genome [Rattus norvegicus] using HISAT2 package. Multiple alignments were allowed for each read sequence (up to 20 by default), with a maximum of two mismatches allowed. HISAT2 also built a database of potential splice junctions.
Transcript abundance estimation and differential expression analysis: Aligned reads of individual samples were assembled using StringTie. Transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome using a proprietary Perl script of LC Sciences (Houston, Texas, U.S.A.). Following transcriptome reconstruction, FPKM reads were evaluated by StringTie, and differential expressed genes were evaluated by edgeR. The differentially expressed mRNAs and genes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1, and with p values < 0.05.
Single-nucleotide Polymorphism (SNP) Analysis: The samtools software was used for calling variants of transcripts, and ANNOVAR was used for SNP/InDel annotation. The function, genome site and type of variation SNPs were also analyzed.
Alternative Splicing Analysis: The software ASprofile was used to identify alternative used to identify alternative splicing events and analyze differential alternative splicing events between samples. The classification of alternative splicing is as follows: SKIP and MSKIP：skipped exon; IR and MIR：intron retained; AE：alternative 5’ or 3’ splice site; TSS：alternative transcription start site; TTS：alternative transcription termination site
Genome_build: GCA_000001895.4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Sep 02, 2020 |
| Last update date |
Sep 03, 2020 |
| Contact name |
Sowmya V Yelamanchili |
| E-mail(s) |
syelamanchili@unmc.edu
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| Phone |
8589266110
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| Organization name |
UNIVERSITY OF NEBRASKA MEDICAL CENTER
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| Department |
Anesthesiology
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| Street address |
984455 Nebraska Medical Center
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| City |
OMAHA |
| State/province |
Nebraska |
| ZIP/Postal code |
68198-4455 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE157348 |
Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure |
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| Relations |
| BioSample |
SAMN15967459 |
| SRA |
SRX9058289 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4762294_F1AO1.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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