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| Status |
Public on Nov 27, 2023 |
| Title |
BS_NCD_rep3 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
organ: BS
strain: C57BL/6J
treatment: NCD
animal: 3
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| Treatment protocol |
normal chow diet (NCD): #8604 Teklad Rodent diet - Envigo, high-fat diet (HFD): #D12492 - Research Diets Inc, synthetic control diet (SCD): #D12450B - Research Diets Inc
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cerebellum, cortex or Brain Stem tissues were homogenized in Trizol reagent (Qiagen) using the OMNI tissue homogenizer (TH) (OMNI International). Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen), according to the manufacturer’s protocol.
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sample Fastq files were aligned to the mouse reference genome GRCm38.p6 (GCA_000001635.8) using TopHat 2.1.1
Mapped reads were filtered for unique mapping to the genome. The number of unique reads mapping to each gene (GencodeM24 annotation) was counted with HTSeq-count (0.9.1, -t exon and –m union)
Assembly: GRCm38.p6 (GCA_000001635.8)
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample
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| Submission date |
Nov 12, 2022 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Melanie Makhlouf |
| E-mail(s) |
mmakhlouf1@sidra.org
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| Organization name |
Sidra Medicine
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| Street address |
Al Gharrafa Street,
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| City |
Ar-Rayyan, Doha, |
| ZIP/Postal code |
PO Box 26999 |
| Country |
Qatar |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE217835 |
Short-term consumption of ultra-processed diets impairs the sense of smell and brain physiology [Brain] |
| GSE218162 |
Short-term consumption of ultra-processed diets impairs the sense of smell and brain physiology |
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| Relations |
| BioSample |
SAMN31700779 |
| SRA |
SRX18242965 |
| 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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