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Sample GSM4622801 Query DataSets for GSM4622801
Status Public on Jun 16, 2023
Title C5_SC
Sample type SRA
 
Source name control_Spinal cord
Organism Mus musculus
Characteristics strain background: C57BL/6
group: Control
tissue: Cervical spinal cord
Treatment protocol Once a day for three consecutive days, 20 μl of 1% SADBE (dissolved in acetone) was applied to the shaved abdomen skin of mice. Five days later, the SADBE treatment group was challenged with 20 μl of 1% SADBE topically applied to the shaved nape skin once daily for three consecutive days, whereas acetone alone was used as a vehicle control.
Extracted molecule total RNA
Extraction protocol Cervical spinal cords were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description control group, biological rep1
Data processing Illumina Casava1.7 software used for basecalling.
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 reads 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.
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 cleanreads 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.
Feature Counts 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 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.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Jun 17, 2020
Last update date Jun 16, 2023
Contact name Xueting Liu
E-mail(s) xuetingliu2019@126.com
Organization name The Second Affiliated Hospital of Guangzhou Medical University
Lab Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology
Street address Changgangdong 250
City Guangzhou
ZIP/Postal code 510260
Country China
 
Platform ID GPL24247
Series (1)
GSE152646 Molecular analysis in SADBE-induced ACD (Allergic contact dermatitis) model
Relations
BioSample SAMN15295626
SRA SRX8564015

Supplementary file Size Download File type/resource
GSM4622801_C5_SC.txt.gz 324.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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