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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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