|
| Status |
Public on May 01, 2024 |
| Title |
SeS, Room Air, PN3, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
genotype: C3H/HeN
dietary selenium_level: 0.4 ppm sodium selenite
oxygen level: FiO2 0.21
age: PN3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the tissues using the Direct-Zol RNA miniprep kit and established protocols from Zymo Research (R2050S, Irvine, CA).
Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Quality check using FastQC
Trimming sequence length using trimmomatic setting LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:40
Mapping using HISAT2 with GRCm39 reference
Raw read count extracted by Featurecounts by setting --countReadPairs -s 2 -p
Normalization and differential test by DeSeq2
Differentially expressed genes with both Log2 folder change >|0.25| and adjust p value<0.05 were selected to further analysis.
Package clusterProfiler with R was used to conduct pathway analysis by using Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database.
Gene set enrichment analysis (GSEA) was conducted by using GSEA 4.1.0.
Assembly: mm39
Supplementary files format and content: sheet named "raw_count" in gene_expression.xlsx file denote raw count of genes in each sample
Supplementary files format and content: sheet named "filtered_normalized_count" in gene_expression.xlsx file denote normalization of genes in each sample
Supplementary files format and content: other sheets denote groupings for analysis.
|
| |
|
| Submission date |
Feb 13, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Trent E Tipple |
| Organization name |
University of Oklahoma Health Sciences Center
|
| Department |
Pediatrics
|
| Lab |
Center for Pregnancy & Newborn Health
|
| Street address |
800 Research Pkwy
|
| City |
Oklahoma City |
| State/province |
Oklahoma |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE255744 |
Se Deficiency Exacerbates Hyperoxia-Induced Lung Injury in Newborn C3H/HeN Mice |
|
| Relations |
| BioSample |
SAMN39939223 |
| SRA |
SRX23618639 |
