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Status |
Public on Nov 22, 2023 |
Title |
AIA1 |
Sample type |
SRA |
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Source name |
knee joint
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Organism |
Rattus norvegicus |
Characteristics |
tissue: knee joint genotype: wt model: AIA
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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 ...
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Submission date |
Dec 16, 2022 |
Last update date |
Nov 22, 2023 |
Contact name |
Yaling Zeng |
E-mail(s) |
ZeroZENGYL@outlook.com
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Organization name |
Macau university of science and technology
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Street address |
Avenida Wai Long, Taipa, Macau, China Avenida Wai Long, Taipa, Macau, China
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City |
Macau |
ZIP/Postal code |
999078 |
Country |
China |
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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 |
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Relations |
BioSample |
SAMN32275693 |
SRA |
SRX18727065 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6846550_AIA1_Clean_Data.txt.gz |
143.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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