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| Status |
Public on Sep 23, 2023 |
| Title |
Uninfected-EVs-6 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Macaca nemestrina |
| Characteristics |
tissue: Brain
group: Uninfected-EVs-6
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| Extracted molecule |
total RNA |
| Extraction protocol |
bdEVs were separated from frozen occipital cortex tissues using our published protocol with minor modifications (Huang et al., 2022a, 2022b, 2020). Before extraction, a small (∼50 mg) piece of tissue was stored at –80°C for later RNA extraction from brain homogenate (BH). bdEV RNAs were extracted by adding Trizol LS (Thermo Fisher 10296028) to 100 μL bdEV resuspension. After phase separation, RNAs were purified by miRNeasy Mini Kit solutions (Qiagen217004) and Zymo-Spin I Columns (Zymo ResearchC1003–50) according to the manufacturer's instructions. BH RNA was extracted by adding Trizol (Thermo Fisher15596018) and homogenizing tissues with Lysing Matrix D (MP Biomedicals116913100) in a benchtop homogenizer (FastPrep-24, MP Biomedicals) at 4.0 m/s for 20 seconds. After homogenization, the supernatant was collected, and RNA was isolated by miRNeasy Mini Kit solutions (Qiagen217004) and Zymo-Spin IIICG Columns (Zymo Research C1006-50-G) following the manufacturer's instructions.
RNA was resuspended in 40 μL Rnase-free water, and 8 µl was used for small RNA libraries construction by the D-Plex Small RNA-seq Kit (Diagenode C05030001). Indexes were attached using the D-Plex Single Indexes for Illumina - Set A (Diagenode C05030010) according to the manufacturer’s protocol.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Yiyao8_EV_combined
EVs6
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| Data processing |
Raw reads were first trimmed from polyA-tails using cutadapt software, and the PCR duplicates were removed by collapsing identical sequences with seqkit. De-duplicated reads were trimmed from the 5'-UMI sequences and size-selected using cutadapt software.
Trimmed and size-selected (>15 nt) readswere aligned to custom-curated hg38 reference transcriptomes using Bowtie,allowing 1 mismatch tolerance (-v 1 option) as follows.
First, reads were mapped to RNA species with low sequence complexity and/or high repeat number:rRNA,tRNA,RN7S,snRNA,snoRNA, scaRNA,vault RNA, RNY, and mitochondrial chromosome (mtRNA).Unmapped reads were aligned sequentially tomature miRNA,pre-miRNA, protein-coding mRNA transcripts (mRNA), and long non-coding RNAs (lncRNAs).Unmapped reads were aligned to the remaining transcriptome (otherncRNAs: mostly pseudogenes and non-protein-coding parts of mRNAs). Finally, all remaining unmapped reads were aligned to the human genome reference (rest hg38) corresponding to introns and intergenic regions.
Assembly: Hg38
Supplementary files format and content: Excel file contains all mapped reads
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| Submission date |
Jul 06, 2023 |
| Last update date |
Sep 23, 2023 |
| Contact name |
Kenneth W. Witwer |
| E-mail(s) |
kwitwer1@jhmi.edu
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| Phone |
4109559770
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Department of Molecular and Comparative Pathobiology
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| Street address |
733 N. Broadway
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL33261 |
| Series (2) |
| GSE236656 |
Small RNA profiles of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology |
| GSE236937 |
RNA profiles of brain tissue |
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| Relations |
| BioSample |
SAMN36345216 |
| SRA |
SRX20928378 |
| 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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