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| Status |
Public on Apr 28, 2023 |
| Title |
Female 24hrs 07 |
| Sample type |
SRA |
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| Source name |
Nucleus accumbens
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| Organism |
Microtus ochrogaster |
| Characteristics |
tissue: nucleus_accumbens
Sex: female
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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 nucleus accumbens. 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 using the NEBNext Ultra RNA Library Prep Kit for Illumina with poly(A) mRNA purification from 300 ng of total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers following the manufacturer’s protocol (#E7530, New England Biolabs, Ipswich, MA, USA). In order to determine the lower limit of detection and verify the linearity of quantification during the statistical analysis of the sequencing data, synthetic RNA Spike-Ins (#4456739, ERCC ExFold RNA Spike-In Mixes, Life technologies, Carlsbad, CA) were added to each sample prior to poly(A) mRNA purification following the recommended dilutions (6 µL of a 1:1000 dilution). Of note, Mix 1 and Mix 2 of the ERCC ExFold RNA Spike-Ins were equally distributed among samples in an exclusive manner. The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) with three serial dilutions ran in duplicates on a CFX384 real-time PCR instrument (Bio-Rad). Finally, the absence of adapters or primers contamination was verified on a Bioanalyzer using a DNA High Sensitivity chip (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 |
FB07
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| Data processing |
Basecalling and demultiplexing was done using Illumina bcl2fastq2 v2.20.0.422
Raw reads were first processed for quality filtering and adapter trimming with fastp (v0.14.1) with adapter trimming, base correction (-p option), and polyX tail trimming (-x option). The final quality of reads was then verified using FastQC (v0.11.7).
Filtered reads were then pseudo-aligned and quantified using Salmon (v0.12) with -g, --numBootstraps 500, --validateMappings, --rangeFactorizationBins 4, --seqBias, and --gcBias parameters.
Genome_build: MicOch1.0 Ensembl Release 93 + GenBank #AF069304.2
Supplementary_files_format_and_content: Matrix of normalized counts for each gene in each sample as computed by DESeq2 (tab-delimited txt file).
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| Submission date |
May 07, 2020 |
| Last update date |
Apr 28, 2023 |
| 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) |
| GSE150080 |
Transcriptomic regulations underlying pair-bond formation and maintenance in the socially monogamous male and female prairie vole |
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| Relations |
| BioSample |
SAMN14850518 |
| SRA |
SRX8289063 |
| 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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