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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 25, 2020 |
| Title |
3103_S2 |
| Sample type |
SRA |
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| Source name |
PWScrm+/p− mutant mice G3
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| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6J
tissue: Hypothalamus
genotype: PWScrm+/p- mutant mice
group: G3
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| Treatment protocol |
The mice were investigated at the beginning of the light period ZT0 (group 1, G1), six hours later at ZT6 (group 2, G2) and at same ZT6 but following 6-hrs of sleep deprivation (SD, group 3, G3).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was homogenizated in Trizol Reagent (Sigma Aldrich). Libraries were prepared using TruSeq polyA mRNA kit (Illumina) according to manufacturer instructions, and sequenced by using the NovaSeq 6000 System (Illumina). Raw sequence reads were quality controlled through FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trimmomatic (v0.38) (http://www.ncbi.nlm.nih.gov/pubmed/24695404). To quantify the transcripts abundances we used Kallisto (v0.44.0) (Bray et al., 2016). Kallisto is also used to build an index from the mouse reference genome (EnsDb.Mmusculus.v79) with default parameters To import and summarize transcript-level abundance of Kallisto, Tximport an R package is used. Differential expression was assessed using DSeq2 (Love et al., 2014). Adjusted p-value less than 0.05 were selected as well as only genes > 2 fold change were considered in the analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequence reads were checked for the quality of sequencing experiment through FASTQC.
Trimmomatic (V0.38) as used as a read trimming tool for Illumina data.
To quantify the transcript abundances, Kallisto (V 0.44.0) is used to build an index from the mouse reference genome (EnsDb.Mmusculus.v79) with default parameters.
To import and summarize transcript-level abundance of Kallisto, Tximport the R package was used.
Differential expression was assessed using DSeq2.
Genome_build: EnsDb.Mmusculus.v79
Supplementary_files_format_and_content: Raw (non normlaized) counts for all genes (also non coding) in all mice
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| Submission date |
Oct 28, 2019 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Alfonso Urbanucci |
| E-mail(s) |
[email protected]
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| Phone |
45048687
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| Organization name |
Oslo University Hospital
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| Street address |
Trondheimsveien 8
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| City |
Oslo |
| State/province |
Oslo |
| ZIP/Postal code |
0560 |
| Country |
Norway |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE139524 |
Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors |
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| Relations |
| BioSample |
SAMN13150980 |
| SRA |
SRX7067251 |
| 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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