|
| Status |
Public on Sep 11, 2023 |
| Title |
Cerebellum_CON_Replicate_5 |
| Sample type |
genomic |
| |
|
| Source name |
Cerebellum
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Cerebellum
Sex: F
group: CON
|
| Treatment protocol |
Edibles were administered prior to the animal’s daily chow to ensure consumption on an empty stomach and to confirm complete ingestion. Animals were slowly titrated up to 2.5mg/7kg/day of THC using published weight-based medical cannabis acclimation recommendations approximately 4 months prior to undergoing time-mated breeding. Each THC-exposed pregnant animal (n=5) continued to consume a daily edible of 2.5mg/7kg/day throughout pregnancy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Placental and fetal tissue DNA was extracted using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).
|
| Label |
Cy3,Cy5
|
| Label protocol |
DNAm was assessed on the MethylationEPIC BeadChips, measuring over 850,000 CpGs at a nucleotide resolution, at the Fred Hutchinson Cancer Research Center Genomics Resource. In brief, 500ng of DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the Illumina-specified instructions.
|
| |
|
| Hybridization protocol |
Converted DNAs were applied to Illumina Infinium Methylation EPIC 8-Sample Beadchips following the Infinium HD Methylation 15019521v01 protocol.
|
| Scan protocol |
Processed BeadChips were scanned using the Illumina iScan+ with ICS v3.3.28 and intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0).
|
| Data processing |
All analysis was performed using R statistical software (version 4.1.1). Data normalization and QC were performed using the minfi and ChAMP packages. We examined density plots of beta values at each preprocessing and filtering step. Stratified quantile normalization preprocessing was performed using minfi to adjust for probe-type bias in beta distributions. Probes previously determined to be functional and valid in Macaca mulatta (referred to as MM_valid) [PMID: 33471557] were retained prior to removing probes with failed detection p-value> 0.01 in >=25% of samples.
|
| |
|
| Submission date |
Jan 26, 2023 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Lyndsey Elizabeth Shorey-Kendrick |
| E-mail(s) |
shorey@ohsu.edu
|
| Phone |
5033465517
|
| Organization name |
Oregon Health and Science University
|
| Street address |
505 NW 185th Ave
|
| City |
Beaverton |
| State/province |
Oregon |
| ZIP/Postal code |
97006 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE223825 |
Chronic Prenatal Delta-9-tetrahydrocannabinol Exposure Adversely Impacts DNA methylation in a Rhesus Macaque Model [methylation] |
| GSE223826 |
Chronic Prenatal Delta-9-tetrahydrocannabinol Exposure Adversely Impacts Placental Function |
|
