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Sample GSM6846555 Query DataSets for GSM6846555
Status Public on Nov 22, 2023
Title R2113
Sample type SRA
 
Source name knee joint
Organism Rattus norvegicus
Characteristics tissue: knee joint
genotype: P53r211* overexpression
model: AIA
Extracted molecule total RNA
Extraction protocol Flash knee joint was harvest and frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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
 
Data processing Illumina Casava1.7 software used for basecalling.
To get high quality clean reads, reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
we aligned reads of all samples to the Rattus norvegicus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Dec 16, 2022
Last update date Nov 22, 2023
Contact name Yaling Zeng
E-mail(s) ZeroZENGYL@outlook.com
Organization name Macau university of science and technology
Street address Avenida Wai Long, Taipa, Macau, China Avenida Wai Long, Taipa, Macau, China
City Macau
ZIP/Postal code 999078
Country China
 
Platform ID GPL25947
Series (1)
GSE221158 Mutant p53R211* specifically suppresses Th17 cell population and ameliorates the arthritic condition in AIA rat via direct binding of TBK1 and inhibition of TBK1-IRF3-STING signaling cascade
Relations
BioSample SAMN32275688
SRA SRX18727070

Supplementary file Size Download File type/resource
GSM6846555_R2113_Clean_Data.txt.gz 144.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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