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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

E-mail(s)

chuchen8715@outlook.com

Organization name

Hebei medical university

Department

Department of Toxicology