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Sample GSM4849244 Query DataSets for GSM4849244
Status Public on Oct 01, 2023
Title CON_1
Sample type SRA
Source name Male mice of the prefrontal cortex of the brain
Organism Mus musculus
Characteristics tissue: the prefrontal cortex of the brain
strain: C57BL/6
age: 30-week
treatment: gavage 0 mg/kg body weight PS NPs
Treatment protocol The PS NPs via oral gavage once per day and for 6 months. The mice were treated with water in control group.
Growth protocol The mice normal eating and drinking. Male, C57BL/6 mice, at 5 weeks old, weight 17 ± 2 g. Before experiment, the animals were fed in the experimental room for 3 days to habituate to the environment of the laboratory. An ambient condition with temperature of 25 ± 2 ℃, relative humidity of 50 ± 2%, and photoperiod of 12 h was maintained throughout the study.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
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.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
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 ( 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).
Supplementary_files_format_and_content: excel,expression profiles
Submission date Oct 22, 2020
Last update date Oct 01, 2023
Contact name chu chen
Organization name Hebei medical university
Department Department of Toxicology
Street address 361 Zhongshan East Road
City Shijiazhuang
State/province Hebei
ZIP/Postal code 050017
Country China
Platform ID GPL17021
Series (1)
GSE159881 Identification of translational microRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing
BioSample SAMN16517662
SRA SRX9345923

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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