 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 09, 2024 |
| Title |
RPE/choroid/sclera complex, AL+PBS-2 |
| Sample type |
SRA |
| |
|
| Source name |
RPE/choroid/sclera complex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: RPE/choroid/sclera complex
genotype: wild type
treatment: ad libitum, Intraperitoneal injection of PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from eye cup utilizing the Trizol/chloroform method according to standard RNA extraction procedure.
RNA libraries for RNA-seq was prepared using TIANSeq Stranded RNA-Seq Kit (Illumina), follwing manufacturers' protocol
Illumina HiSeq PE150
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
In the process of comparison (align) with the reference group, we choose the reference genome of the species or known transcriptome data (e.g., full-length transcriptome spliced by three-generation technology). The comparison tool was chosen to be HISAT2, which uses a modified BWT algorithm.
The analysis was quantified using the StringTie tool based on the positional information of the gene ratio on the reference genome, thus counting the number of reads covered by each gene from the start to the end range.
To screen the samples for genes with significantly different expression levels in different states.Differential expression analysis was performed by DESeq2 (with duplicate samples) or edgeR (without duplicate samples), and the input data were the reads count expression quantified by StringTie. DESeq2 is divided into three main parts.1) firstly, the original readcount is normalized, mainly for the correction of sequencing depth; 2) then the statistical model is used to calculate the probability of hypothesis testing (pvalue); 3) finally, multiple hypothesis testing is performed.3) Finally, multiple hypothesis testing correction is performed to obtain the FDR value (false discovery rate, padj is its common form). The conventional criteria for screening differential genes are |log2(FoldChange)| > 1 & padj<0.05, and if the number of differential genes is too small under this screening threshold, |log2(FoldChange)| >0.5 & pvalue<0.05 were chosen. both are commonly used screening criteria, and the screening criterion for the current project was |log2( FoldChange)| > 1 & padi<0.05.
We used clusterProfiler software to perform GO function enrichment analysis, KEGG pathway enrichment analysis, etc. on the differential gene sets. The enrichment analysis results are enriched for all differential gene sets, up-regulated differential gene sets, and down-regulated differential gene sets for each differential comparison combination.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 08, 2024 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Jingzhen Li |
| E-mail(s) |
lijingzhen@xzhmu.edu.cn
|
| Phone |
15927233895
|
| Organization name |
xuzhou medical university
|
| Department |
Life science
|
| Lab |
Jiangsu Key Laboratory of Brain Disease Bioinformation
|
| Street address |
huang shan road
|
| City |
xu zhou |
| ZIP/Postal code |
221000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE271791 |
Intermittent fasting alleviates photoreceptor degeneration and retina inflammation in oxidative stress-induced model of Age-Related Macular Degeneration |
|
| Relations |
| BioSample |
SAMN42380696 |
| SRA |
SRX25247512 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
