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| Status |
Public on Apr 03, 2024 |
| Title |
Saline, Rep2 |
| Sample type |
SRA |
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| Source name |
nucleus accumbens
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| Organism |
Microtus ochrogaster |
| Characteristics |
tissue: nucleus accumbens
treatment: Saline
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen AllPrep
NEBNext Ultra Directional RNA with magnetic mRNA isolation
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Lib30_S14
IOL_GeneCounts.csv
IOL_IsoformCounts.csv
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| Data processing |
Trimgalore was used for adapter trimming and quality control
Kallisto was used for pseudo-alignment and quantification followed by DESeq2 for gene-level differential expression
STAR2 and Stringtie were used for splice-aware alignment and subsequent novel transcript identification, followed by IsoformSwitchAnalyzeR for differential transcript usage
Assembly: MicOch v1.0, Ensembl release version 96
Supplementary files format and content: IOL_GeneCounts.csv (kallisto-based gene-level quantification)
Supplementary files format and content: IOL_IsoformCounts.csv (novel transcript quantification)
Supplementary files format and content: MicOch_stringtie_merged_transcripts.gtf (StringTie novel transcript assembly)
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| Submission date |
Aug 14, 2023 |
| Last update date |
Apr 03, 2024 |
| Contact name |
Joshua Danoff |
| E-mail(s) |
jsd5zs@virginia.edu
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| Organization name |
University of Virginia
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| Street address |
485 McCormick Road
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
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| Platform ID |
GPL31149 |
| Series (2) |
| GSE240832 |
Maternal oxytocin treatment at birth increases epigenetic age in male offspring [RNA-seq] |
| GSE240856 |
Maternal oxytocin treatment at birth increases epigenetic age in male offspring |
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| Relations |
| BioSample |
SAMN36985366 |
| SRA |
SRX21362379 |
| 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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