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| Status |
Public on Mar 03, 2021 |
| Title |
Sham #5 |
| Sample type |
SRA |
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| Source name |
Tail-vein plasma
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: Adult
group: Sham
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was drawn from the lateral tail-vein under isoflurane anesthesia, into Microtainer K2 EDTA-tubes. The blood samples were thoroughly mixed with EDTA and placed on ice. Centrifugation was performed immediately at 1300g for 10 min (+4°C) to obtain plasma. RNA was isolated from 200 µL plasma using the miRNeasy serum/plasma kit.
Small RNA libraries were prepared with QIASeq miRNA library kit for Illumina NGS systems.
Small RNA-Seq. Single-end sequencing of 75 bp reads performed at a depth of 12M, with one sample/lane in the Illumina NextSeq 550.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
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| Description |
20657-015
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| Data processing |
Raw sequencing data was analysed with the Qiagen Geneglobe Data analysis center (DAC), a freely available web resource to analyze data from Qiagen’s QIASeq NGS library kits (https://geneglobe.qiagen.com/in/analyze/).
Primary quantification of read counts was performed in the DAC, which involved the following steps: (i) trimming of the 3’-adapter and low-quality bases using cutadapt, (ii) identifying the insert sequences and unique molecular indices (UMIs) (reads with <16 bp insert sequences or < 10 bp UMI sequences were discarded), (iii) alignment of the processed reads to the rat reference genome RGSC Rnor_6.0 with a sequential alignment strategy using bowtie (perfect match to miRBase mature, miRBase hairpin, noncoding RNA, mRNA and other RNA, and ultimately a second mapping to miRBase mature, where up to two mismatches are tolerated). Annotation of the miRNAs in the DAC portal was performed with miRBase v21.
Genome_build: RGSC Rnor_6.0, miRBase v21
Supplementary_files_format_and_content: Compiled matrix table with raw counts for every miRNA in every sample
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| Submission date |
Oct 05, 2020 |
| Last update date |
Mar 03, 2021 |
| Contact name |
Shalini Das Gupta |
| E-mail(s) |
[email protected]
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| Organization name |
University of Eastern Finland
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| Department |
A.I.Virtanen Institute
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| Street address |
Neulaniementie 2, P.O.B. 1627
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE159011 |
Plasma miR-9-3p and miR-136-3p levels as novel diagnostic biomarkers for mild traumatic brain injury |
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| Relations |
| BioSample |
SAMN16366227 |
| SRA |
SRX9242917 |
| 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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