|
| Status |
Public on Aug 17, 2022 |
| Title |
Frontal-Cortex_Saline_3-hours-post-injection_6 |
| Sample type |
SRA |
| |
|
| Source name |
Frontal Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Frontal Cortex
treatment: Saline
timepoint: 3 hours post-injection
cage: 6
extraction pool: D
|
| Treatment protocol |
Ten-week-old chow-fed male C57BL/6J mice (group-housed) were randomized into one of four treatment groups (n=8 per group) as follows: Group 1: A single intraperitoneal injection of 3 mg/kg psilocybin, followed by tissue harvest 3 hours after treatment. Group 2: A single intraperitoneal injection of isotonic saline followed by tissue harvest 3 hours after treatment. Group 3: A single intraperitoneal injection of 3 mg/kg psilocybin followed by tissue harvest four weeks after treatment. Group 4: A single intraperitoneal injection of isotonic saline followed by tissue harvest 4 weeks after treatment.
Mice received a single intraperitoneal injection according to their grouping, and were sacrificed (decapitation) according to the above schedule. Prefrontal cortex and whole hypothalamus were immediately dissected out and flash frozen on dry ice. Mice were euthanized in the morning, four hours after the onset of the light phase, to ensure minimal diurnal variation in gene expression. Dissected brain regions were stored at -80⁰C until isolation of RNA was performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using an RNeasy mini kit (Qiagen, #74106) according to the manufacturer’s protocol
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Fragment Analyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.7 billion reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were generated using bcl2fastq2 v. 2.20.0
Reads were aligned to the GRCm38 primary assembly using STAR v. 2.7.2b against a reference built using the GENCODE vM25 gene model
Aligned reads were counted against the same gene model using featureCounts v. 1.6.2 counting only reads where both ends mapped to the same strand
Counts from the two sequencing runs were added together
Assembly: mm10
Supplementary files format and content: csv file with read counts
|
| |
|
| Submission date |
Jul 27, 2022 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Lars Roed Ingerslev |
| E-mail(s) |
ingerslev@sund.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
NNF Center for Basic Metabolic Research
|
| Lab |
Integrative Physiology
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE209859 |
Acute and long-term effects of psilocybin on energy balance and feeding behavior in mice |
|
| Relations |
| BioSample |
SAMN29992286 |
| SRA |
SRX16687716 |
