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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 12, 2024 |
| Title |
ZT17, OLM [G610_52_RS36_S52] |
| Sample type |
SRA |
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| Source name |
dorsal hippocampus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
tissue: dorsal hippocampus
treatment: Trained in OLM at ZT17 (12a), sac'd 60m later
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested with the Rneasy mini kit (Qiagen). 250ng of total RNA was used to contstruct sequencing libraries
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep kit following manufacturer protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Data quality was inspected using FastQC reports.
Data was mapped to the mouse reference genome and visualized in IGV.
Reads mapping to the genes were counted using featureCounts software.
Read count normalization and differential expression were performed using DESeq2 package in R.
Circadian genes were identified with JTK algorithm in the Metacycle program, specifying 24-hour window.
Over representation analysis was performed in R to identify the enriched KEGG and Reactome pathways.
Assembly: Mus musculus, GRCm38 build
Supplementary files format and content: Tab delimited file with gene-level raw read counts for each sample
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| Submission date |
Jan 12, 2023 |
| Last update date |
Jan 12, 2024 |
| Contact name |
Aswathy Sebastian |
| E-mail(s) |
azs13@psu.edu
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| Phone |
5204613475
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| Organization name |
PennState
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| Street address |
University Park
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| City |
State College |
| ZIP/Postal code |
16801 |
| Country |
USA |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE222744 |
The clock gene Per1 may exert diurnal control over hippocampal memory consolidation |
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| Relations |
| BioSample |
SAMN32710901 |
| SRA |
SRX19016575 |
| 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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