|
| Status |
Public on May 05, 2023 |
| Title |
Brain coronal slice (1.5 mm posterior to the bregma) transcriptome-ZT4_F_RHY |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
strain: C57BL/6J
Sex: Female
genotype: WT
treatment: Rhynchophylline 100 mg/kg
|
| Treatment protocol |
Rhynchophylline (RHY, 100 mg/kg; administered with a volume of 10 mL/kg) or Saline (NaCl 0.9 %) intraperitoneal injections at ZT0 or ZT11
|
| Growth protocol |
Habituation to individual cage for 10 days; housing with a 12h light:12h dark cycle with food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics protocol CG000240-Rev C
10X Genomics protocol CG000160-Rev A (Hematoxylin-Eosin staining)
10X Genomics protocol CG000239-Rev D
Paired-end dual indexed RNA sequencing with Illumina NovaSeq6000 SP100 sequencer (Genome Quebec Innovation Centre, Montreal, Canada), at a sequencing depth of approximately 150M read pairs per sample. RNAseq was performed according to instructions of 10x Genomics for the Visium Spatial Gene Expression kit: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BAM file created by running the original sequencing file with the ''spaceranger count'' pipeline.
|
| Data processing |
SpaceRanger1.2.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: ''spaceranger count'' pipeline and obtain h5 matrix and spatial information on the reads, and can also be processed with other RNAseq platforms, softwares and commands.
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
May 07, 2023 |
| Contact name |
Valerie Mongrain |
| E-mail(s) |
valerie.mongrain@umontreal.ca
|
| Phone |
514 338-2222 3323
|
| Organization name |
CRCHUM
|
| Department |
Research center
|
| Lab |
Tour Viger, local R09-720
|
| Street address |
333 rue Saint-Antoine Est
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H2X1R9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218537 |
Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics (additional files) |
|
| Relations |
| Affiliated with |
GSM6704281 |
| BioSample |
SAMN31836176 |
| SRA |
SRX18346554 |
