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| Status |
Public on Feb 28, 2023 |
| Title |
THC/SIV IH69 |
| Sample type |
SRA |
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| Source name |
Basal ganglia
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| Organism |
Macaca mulatta |
| Characteristics |
treatment: SIV Infected with THC
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| Treatment protocol |
SIV-infected rhesus macaques were treated with Vehicle or delta-9-tetrahydrocannabinol at 0.32 mg/kg for 6 months post SIV infection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from basal ganglia tissues at necropsy using the miRNeasy kit (Qiagen Inc).
Transcriptome profiling by RNA-seq and data analysis were performed by Novogene (Sacremento, CA). cDNA library construction and sequencing were performed by Novogene Co. Ltd, Beijing, CA (http://www.novogene.cn/). For library construction, ~3 μg of total RNA from each sample was used to enrich mRNA with the poly-T oligo-attached magnetic beads. The purified mRNA was then randomly cleaved into small fragments using NEBNEXT RNA fragmentation buffer following the manufacturer’s instructions. First-strand cDNA was synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis by nick translation was subsequently performed using E coli DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. The final cDNA library was prepared after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. The cDNA fragments of preferentially 250−300 bp in length were selected using with AMPure XP system (Beckman Coulter, Beverly, U.S.A.) and PCR amplified using Phusion High-Fidelity DNA polymerase (NEB, Beijing, China), Universal PCR primers and Index (X) Primer. PCR products were then purified using AMPure XP system (Beckman Coulter, U.S.A.), and library quality was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, U.S.A.). The clustering of the index-coded samples was performed on a cBot Cluster Generation System, using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
IH69
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| Data processing |
Raw reads were first processed through perl scripts to remove reads containing adapter or -N or with base quality score lower than 20. At the same time, the Q20, Q30 and GC contents of the clean data were calculated. The clean reads were aligned to the genome assembly of Macaca mulatta 10 (https://www.ncbi.nlm.nih.gov/genome/215?genome_assembly_id=468623) using TopHat2, and read numbers mapped to each gene were calculated using the HTSeq program. The fragments per kilobase of transcript sequence per million base pairs of each gene were determined by the length of the gene and read counts mapped to this gene. Differential expression analyses of VEH or THC-treated SIV-infected RMs and control groups were performed using the DESeq of R package. Genes with a P-value <0.05 and |log2 fold change| > 0.585 were defined as differentially expressed.
Assembly: Macaca_mulatta.Ensembl_release_76
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Jul 05, 2022 |
| Last update date |
Feb 28, 2023 |
| Contact name |
Mahesh Mohan |
| E-mail(s) |
mmohan@txbiomed.org
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| Organization name |
Southwest National Primate Research Center
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| Department |
Host Pathogen Interaction Program
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| Lab |
12/106
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| Street address |
8715 West Military Road
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| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78227 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (2) |
| GSE207518 |
Transcriptome profiling of Basal ganglia tissue from chronically SIV infected rhesus macaques |
| GSE220783 |
Cannabinoid modulation of gene and microRNA expression in brain (basal ganglia) during chronic HIV/SIV infection |
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| Relations |
| BioSample |
SAMN29509689 |
| SRA |
SRX16033207 |
| 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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