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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 18, 2024 |
| Title |
Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 2 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
genotype: WT
diet: High Fat High Sugar Time Restricted Feeding
time: zt15
treatment: ORM training +12h
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using pS6-TRAP protocol. 50ng of TRAP purified mRNA was used for the construction of sequencing libraries.
TRAP-mRNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep (Illumina, 20040534) and IDT for Illumina RNA UD Indexes Set B and Set C (Illumina, 20040554 and 20040555) following manufactured's protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
HFS.TRF.ORM12h-r2
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| Data processing |
workflow Nextflow (v21.10.6) and nf-core/rnaseq (v3.6) pipeline onto genotoul bioinformatics platform Toulouse
Sequence reads were trimmed for adaptor/low quality sequence using trimgalore (v0.6.7) and cutadapt (v3.4)
Trimmed sequence reads were mapped to GRCm39/mm109 using HISAT2 aligner (v2.2.0) and reads mapped to unique transcripts were counted with FeatureCounts (Subread v2.0.3) annotation module
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
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| Submission date |
May 17, 2024 |
| Last update date |
Nov 18, 2024 |
| Contact name |
jean-christophe Helbling |
| E-mail(s) |
[email protected]
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| Phone |
0664278921
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| Organization name |
INRAE
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| Department |
Alimentation humaine
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| Lab |
NutriNeuro
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| Street address |
Université de Bordeaux - INRAE, Rue Leo Saignat, 146
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| City |
BORDEAUX |
| State/province |
--None-- |
| ZIP/Postal code |
33000 |
| Country |
France |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE267751 |
Time-restricted feeding prevents memory impairments induced by obesogenic diet consumption in mice, in part through hippocampal thyroid hormone signaling. |
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| Relations |
| BioSample |
SAMN41436871 |
| SRA |
SRX24591945 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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