|
| Status |
Public on Jan 08, 2024 |
| Title |
Run2-MA524L |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Liver
treatment: Diet A - 0.02 mg/kg bw/day 3-methylfuran
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from flash frozen tissue samples using Qiagen miRNeasy kits. 20mg of frozen liver was placed in pre-filled tube containing Qiazol reagent and Zirconium beads, then homogenized 2 x for 20 seconds. Subsequent steps were followed as per manufacture's instructions.
3-methylfuran cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol. Furan cDNA libraries were prepared with the Illumina Stranded mRNA prep kit (updated release).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0)
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2
|
| |
|
| Submission date |
Dec 07, 2023 |
| Last update date |
Jan 08, 2024 |
| Contact name |
Lauren E Carter |
| E-mail(s) |
lauren.carter@hc-sc.gc.ca
|
| Organization name |
Health Canada
|
| Department |
251 Sir Frederick Banting Driveway
|
| Street address |
251 SIR FREDERICK BANTING
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE249626 |
Comparative genomic analysis of Fischer F344 rat livers exposed for 90 days to 3-methylfuran or its parental compound furan. |
|
| Relations |
| BioSample |
SAMN38716840 |
| SRA |
SRX22818075 |
