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| Status |
Public on Oct 05, 2022 |
| Title |
attackers_A1_nucleus_accumbens |
| Sample type |
SRA |
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| Source name |
nucleus_accumbens
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| Organism |
Microtus ochrogaster |
| Characteristics |
group: attackers
tissue: nucleus_accumbens
subject_id: A1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial preoptic nucleus, nucleus accumbens, and lateral septum. Total RNA was then extracted using TRI-Reagent according to the manufacturer's protocol (Molecular Research Center, #TR 118), followed by DNAse I treatment to remove any eventual DNA contamination and clean-up (RNA Clean & Concentrator, Zymo Research, Irvine, CA, USA).
RNA-seq libraries were prepared by the Florida State University NGS Library Facility following poly(A) mRNA purification from total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers (New England Biolabs, Ipswich, MA, USA). The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) and the absence of adapters or primers contamination was verified on an Agilent TapeStation (Agilent Technologies, Santa Clara, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
A1N
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| Data processing |
Basecalling and demultiplexing was done using Illumina bcl2fastq v2.20.
Raw reads were first processed for quality filtering and adapter trimming with fastp (v0.20.0) with adapter trimming, base correction (-p option), and polyX tail trimming (-x option). The final quality of reads was then verified using FastQC (v0.11.8).
Filtered reads were then pseudo-aligned and quantified using Salmon (v0.14.1) with -g, --numBootstraps 1000, --validateMappings, --rangeFactorizationBins 4, --seqBias, --gcBias, and --recoverOrphans parameters.
Genome_build: MicOch1.0 Ensembl Release 97 + GenBank #AF069304.2
Supplementary_files_format_and_content: Matrix of reads counts (not normalized) for each gene in each sample as computed by DESeq2 (tab-delimited txt file).
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| Submission date |
Dec 05, 2021 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Mohamed Kabbaj |
| E-mail(s) |
[email protected]
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| Phone |
850-644-4930
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| Organization name |
Florida State University
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| Department |
Biomedical Sciences
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| Street address |
1115 W Call St
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| City |
Tallahassee |
| State/province |
Florida |
| ZIP/Postal code |
32306 |
| Country |
USA |
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| Platform ID |
GPL28499 |
| Series (1) |
| GSE190213 |
Transcriptomic analysis of paternal behaviors in prairie voles |
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| Relations |
| BioSample |
SAMN23668628 |
| SRA |
SRX13320558 |
| 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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