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| Status |
Public on Aug 21, 2020 |
| Title |
Control_2 [miRNA] |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Rattus norvegicus |
| Characteristics |
sample type: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: Rattus_norvegicus Ensembl relaese-94
Supplementary_files_format_and_content: excel, expression profiles
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| Submission date |
Jun 25, 2020 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Xue Liu |
| E-mail(s) |
liuxue0081985@126.com
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| Organization name |
The Affiliated Hospital of Shandong University of TCM
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| Street address |
Wenhua West Road
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| City |
JiNan |
| State/province |
ShangDong |
| ZIP/Postal code |
250014 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE153294 |
Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq] |
| GSE153296 |
Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis |
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| Relations |
| BioSample |
SAMN15373812 |
| SRA |
SRX8620601 |
| 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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