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Sample GSM4422825 Query DataSets for GSM4422825
Status Public on Mar 20, 2023
Title PCN7: PCN rep3
Sample type SRA
 
Source name Kidney
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: kidney
age: 8 weeks
genotype: wild type
Extracted molecule total RNA
Extraction protocol Male C57BL/6 wild-type mice (8 week old) were randomly divided into 4 groups with 6~8 animals each: corn oil + saline (CON), PCN + saline (PCN), corn oil + cisplatin (CIS) and PCN + cisplatin (CIS+PCN). Two groups of mice (CIS and CIS+PCN) were pretreated via oral gavage daily with PCN (40 mg/kg) for 4 days and the additional two groups (CON and CIS) were administrated with equal volume of corn oil for 4 days. A single nephrotoxic dose of cisplatin (20 mg/kg) was administrated intraperitoneally (i.p.) to CIS and CIS+PCN groups on Day 4, and then the daily corn oil or PCN treatment was continued for 3 days in all groups. Mice were sacrificed 4 days after cisplatin injection.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing read containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
 
Submission date Mar 20, 2020
Last update date Mar 20, 2023
Contact name Zhilin Luan
E-mail(s) zhilin_luan@sina.com
Phone +8641186118982
Organization name Advanced Institute for Medical Sciences, Dalian Medical University
Street address 9 W., S. Lvshun Blvd.
City Dalian
State/province China
ZIP/Postal code 116044
Country China
 
Platform ID GPL21103
Series (1)
GSE147256 Pregnane X Receptor (PXR) protects against cisplatin-induced acute kidney injury
Relations
BioSample SAMN14410487
SRA SRX7958074

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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