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| Status |
Public on May 11, 2021 |
| Title |
Amygdala sample from subject 38 |
| Sample type |
SRA |
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| Source name |
Brain - Amygdala
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| Organism |
Macaca mulatta |
| Characteristics |
treatment: OvH-HT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA and RNA were extracted from each brain region using the All-Prep DNA/RNA/miRNA Universal kit (Qiagen Sciences Inc, Germantown, MD) following the manufacturer’s recommendations. Briefly, each brain section was pulverized, and ~30 mg of tissue was used for DNA/RNA isolation.
For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA, USA).
RNA-Seq: The libraries were sequenced on a HiSeq 4000 (Genomics & Cell Characterization Core Facility, University of Oregon) using a paired-end run (2 × 150 bases).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S38_AMYG
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| Data processing |
Sequences raw files were imported into ONPRC's Prime‐Seq, LabKey Server‐based system (Nelson EK, Piehler B, Eckels J, et al. LabKey server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics. 2011;12(1):71.)
Quality control of the sequences was verified through FastQC (v. 0.1.1.2)
Illumina adapter were removed and 3' read ends were trimmed using Trimmomatic (Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114‐2120)
Reads were aligned to the Rhesus Macaque reference genome (Mmul_10, INSDCA Assembly GCA_003339765.3) using the STAR aligner (v. 2.7.3a) allowing for maximum of 3 mismatches and only unique alignments.
Per‐sample gene count tables were generated by STAR using Ensembl gene annotations (Ensembl.Mmul_10.100) and were merged to form a single gene count matrix.
Genes with at least 0.2 CPM (for Occipital Cortex and Amygdala) and 0.3 CPM (in Prefrontal Cortex and Hippocampus) across samples were retained for further analysis. These thresholds translate into roughly 10 reads per minimum library size (10/minimum library size in millions)
Upper quartile normalization was performed using the edgeR (v. 3.28.0) Bioconductor package.
Differential expression (DE) between the OvH and OvH-HT groups was determined using edgeR’s Fisher’s exact test function, with the option of “tagwise” dispersion.
Genome_build: Mmul10
Supplementary_files_format_and_content: E2_UQ_normalized_counts.csv (upper-quartile normalized counts): format=comma-delimited, content= normalized gene counts with genes in rows and samples in columns
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| Submission date |
May 10, 2021 |
| Last update date |
May 11, 2021 |
| Contact name |
Priscila Darakjian |
| E-mail(s) |
darakjia@ohsu.edu
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| Organization name |
Oregon Health and Science University
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| Department |
Behavioral Neuroscience
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| Street address |
3181 SW Sam Jackson Park Road, L470
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL23949 |
| Series (1) |
| GSE174153 |
Effects of estradiol supplementation on the brain transcriptome of old rhesus macaques maintained on an obesogenic diet. |
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| Relations |
| BioSample |
SAMN19092506 |
| SRA |
SRX10828191 |
| 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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