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| Status |
Public on Dec 14, 2021 |
| Title |
Animal 16172, PBMC, index GTAGAG, 1st run [B6_PBMC] |
| Sample type |
SRA |
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| Source name |
Animal 16172, PBMC, index GTAGAG
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| Organism |
Papio hamadryas |
| Characteristics |
tissue: PBMC
animal id: Animal 16172
molecule: miRNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Baboons were sedated with ketamine (10mg/kg) prior to collection of blood in Cell Preparation Tubes (Becton-Dickinson, Franklin Lakes, NJ, USA), anesthetized (1-2% isoflurane), and euthanized via either intravenous injection of pentobarbital (>100mg/kg) or exsanguination while under general anesthesia. Necropsy was performed to obtain brain tissue. PBMCs were isolated according to the manufacturers’ protocol. Brain regions were dissected from fresh tissue, placed in a cryovial, and flash frozen in liquid nitrogen. All samples were stored at -80°C. Total RNA was isolated from PBMCs and brain regions using the miRNeasy Mini Kit (Qiagen, Germantown, MD).
Small RNA sequencing libraries were prepared using the Illumina Truseq Small RNA Sample Prep Kit.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Raw sequence reads were obtained using Illumina's Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base calling by Pipeline Bustard Module.
Extracted sequence reads were aligned (Bowtie), normalized, annotated and abundance determined using mirDeep2.
Genome_build: miRbase v21
Supplementary_files_format_and_content: Excel spreadsheet with normalized read counts for 362 miRNAs.
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| Submission date |
Dec 10, 2021 |
| Last update date |
Dec 14, 2021 |
| Contact name |
Melanie Anita Carless |
| E-mail(s) |
[email protected]
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| Organization name |
The University of Texas at San Antonio
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| Street address |
One UTSA Circle
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| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78249 |
| Country |
USA |
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| Platform ID |
GPL15440 |
| Series (1) |
| GSE190675 |
Blood-based miRNA biomarkers as correlates of brain-based miRNA expression |
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| Relations |
| BioSample |
SAMN23891614 |
| SRA |
SRX13377313 |
| 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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