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Sample GSM4852486 Query DataSets for GSM4852486
Status Public on Oct 02, 2023
Title CON_1
Sample type SRA
Source name Male mice, prefrontal cortex of the brain
Organism Mus musculus
Characteristics strain: C57BL/6
age: 30-week
treatment: gavage 0 mg/kg body weight PS NPs
tissue: prefrontal cortex of the brain
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. 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 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Illumina Casava1.8 software used for basecalling.
First, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
Then aligned reads of samples to the reference genome using Hisat2 package.
The mapped reads of each sample were assembled using StringTie, and all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI were used to identified circRNAs.
Genome_build: mus musculus ensembl release-96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date Oct 24, 2020
Last update date Oct 02, 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 GPL24247
Series (1)
GSE160012 Identification of translational ncRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing
BioSample SAMN16538055
SRA SRX9352667

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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