Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics (additional files)
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Summary:
Here, we investigated the effects of Rhynchophylline (RHY) on the mouse brain spatial transcriptome. More precisely, we injected male and female mice intraperitoneally with either saline (NaCl) or RHY, either at Zeitgeber time (ZT referring to time in hour after light onset) 0 or ZT0 and ZT11. Brains were sampled at ZT4 or ZT14, respectively, and immediately frozen embedded in OCT. Brains were treated and libraries were prepared according to 10x Genomics protocols for Visium Spatial Gene Expression. Sequencing was conducted by Genome Quebec (Montreal, Quebec, Canada). Findings reveal molecular routes by which RHY acts on the brain in a sleep-relevant context. Please cite the original paper when using these data (Ballester Roig et al., Biol Direct, 2023) and see also the submission GSE217058.Overall design:
Brain transcriptome measured 3 to 4 hours after one or two intraperitoneal injection of Rhynchophylline (RHY, 100 mg/kg) conducted at two different times of the day (ZT0 or ZT0 and ZT11) in male and female C57BL/6J mice that were kept under a 12 h light:12 h dark cycle. The same measurements were conducted in mice receiving saline (acting as controls). The total number of samples for this project is thus 8 (one female receiving RHY at ZT0, one female receiving saline at ZT0, one female receiving RHY at ZT0 and ZT11, one female receiving saline at ZT0 and ZT11, one male receiving RHY at ZT0, one male receiving saline at ZT0, one male receiving RHY at ZT0 and ZT11, one male receiving saline at ZT0 and ZT11). The brain transcriptome was quantified with the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics). Original fastq files and processed files were uploaded at GSE217058. However, raw fastq files for two samples were damaged during file storage and are missing (i.e., female receiving RHY at ZT0 and female receiving saline at ZT0 and ZT11). Here we provide the BAM files of these two samples (ZT4_F_RHY and ZT14_F_Saline) which were created with the pipeline ''spaceranger count'' with the original uncorrupted fastq files. These BAM files can be used to reconstitute the corresponding fastq files using the bamtofastq tool.Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Mus musculus(mm10)
Tissues:
Brain
Sex:
FemaleCitation:
Ballester Roig, Maria Neus et al. “Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics.” Biology direct vol. 18,1 21. 5 May. 2023, doi:10.1186/s13062-023-00377-7Submission date: 2022-11-22Update date: 2023-08-08
Sample number: 2Section number: 2
Contributors
Mongrain, Valerie; Ballester Roig, Maria Neus; Dufort-Gervais, Julien
Accessions
GEO Series Accessions:
GSE218537