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| Status |
Public on Nov 26, 2024 |
| Title |
BALBc mice, 8 weeks, female, 3 days after CP, VitA-enriched diet, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
urinary bladder
|
| Organism |
Mus musculus |
| Characteristics |
tissue: urinary bladder
genotype: wild type
treatment: cyclophosphamide (150 mg/kg b.w.), Vitamin A-enriched diet (566081UI retinyl-acetate per kilogram)
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| Treatment protocol |
Half of the mice's diet was changed to Vitamin A-enriched diet (566081UI retinyl-acetate per kilogram) one week before application (i.p. injection) of cyclophosphamide (CP;150 mg/kg b.w.) or saline (S). Mice injected with saline served as controls. Eutanisations were executed one and three days after CP or S application.
|
| Growth protocol |
Animales were housed in groups of 3 animals in polyacrylamide cages at constant humidity (55%) and temperature (22°C) with water and food ad libitum and 12h/12h light-dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRI Reagent (VWR) and PeqGOLD Total RNA Kit (VWR). Library preparation was performed by Novogene Co., Ltd, using at least 0.5 ug high-quality total RNA input per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer’s recommendations
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: H2
|
| Data processing |
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including Hisat2, FeatureCounts and Novogene's wrapped scripts.
High quality reads were aligned to mouse (Ensembl GRCm39) reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. The fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups (CP1dvsCP1d+VitA, FR1dvsFR1d+VitA, CP3dvs>CP3d+VItA; three replicates per group) was performed using DESeq2 R package (1.20.0). P value was calculated using the negative binomial distribution and the resulting p values were adjusted using the Benjamini-Hochberg’s approach for controlling the false discovery rate.
The clusterProfiler (v. 3.8.1) software was used for enrichment analysis of differentially expressed genes, including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome database
Assembly: GRCm39
Supplementary files format and content: excel file includes counts for each gene for each sample (gene_count.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample (gene_fpkm.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of CP1d group vs CP1d+VitA group (CP1dvsCP1d_VitA_deg_all.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of FR1d group vs FR1d+VitA group (FR1dvsFR1d_VitA_deg_all.xls_deg_all.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of CP3d group vs CP3d+VitA group (CP3dvsCP3d_VitA_deg_all.xls)
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| |
|
| Submission date |
Nov 21, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Brina Dragar |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Ljubljana, Faculty of Medicine
|
| Department |
Institute of Cell Biology
|
| Street address |
Vrazov trg 2
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE282487 |
Effect of dietary increased Vitamin a on urothelial regeneration after Cyclophosphamide induced injury in mice |
|
| Relations |
| BioSample |
SAMN44854944 |
| SRA |
SRX26797809 |
