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Sample GSM8496218

Query DataSets for GSM8496218

Status

Public on Sep 04, 2024

Title

Con4

Sample type

SRA

Source name

mPFC

Organism

Mus musculus

Characteristics

tissue: mPFC
genotype: Gpr158flox/flox
treatment: Naive

Growth protocol

All mice used in this study were on a C57Bl/6J background and housed in a pathogen-free SPFII facility with constant temperature (23±1 ℃) and controlled humidity (50±10%) on a 12h/12h light/dark cycle (lights on at 07:00) in the Center of Laboratory Animal Science, Southern University of Science and Technology (SUSTec), China. Mice were maintained at a group of 4 to 5 in a clear plastic cage, and had free access to drinking water and standard food. All experiments were conducted according to the NIH Guide for the Care and Use of Laboratory Animals (Eighth Edition, 2011). The experimental procedures were approved by the Animal Care Committee at the SUSTec, China.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the mPFC of adult male CaKO mice and the littermate Gpr158fl/fl controls with Tripure Isolation Reagent (Roche, Germany). Briefly, approximately 100 ng of total RNA sample was used for poly-A mRNA selection using oligo(dT) beads and subjected to thermal mRNA fragmentation. The fragmented mRNA samples were subjected to cDNA synthesis and were further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. The final libraries were bar-coded, purified, pooled together in equal concentrations, and subjected to 100bp paired-end sequencing on Illumina Novaseq-6000 sequencer.
RNA library was constructed with stardard illumina protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

RNA-sequencing analysis was carried out using the Illumina NovaSeq 6000 platform (Novogene, China). Paired-end clean reads were aligned to the mouse reference genome (Ensemble_GRCm38.90) with TopHat (version 2.0.12), and HTSeq-count (version 0.6.1) was used to quantify the mRNA levels.
FASTQ files were mapped to align the reads. Read count normalizations and group comparisons were carried out with DESeq2 (v1.30.1), using the Wald test for significance testing. Genes with low counts were filtered, if at least half the samples have less than 20 normalized reads. For differential expression study, the results obtained after DESeq2 comparison were selected for further analysis and filtered at False discovery rate (FDR)- adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: text files includiing FPKM values for each sample

Submission date

Sep 04, 2024

Last update date

Sep 04, 2024

Contact name

Shoupeng Wei

E-mail(s)

shoupengwei2015@gmail.com

Organization name

The Seventh Affiliated Hospital, Sun Yat-Sen University

Street address

628 Zhenyuan Rd