|
| Status |
Public on Jun 18, 2022 |
| Title |
L3209_B2D |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J mice, B2-Deficient Diet, 1 Month
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: WT
treatment: B2-Deficient Diet
|
| Treatment protocol |
Mice were fasted overnight before harvest. Mice fed FF (Ctrl_FF and B2D_FF) were fasted overnight and administered FF 2 hours before harvest
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total Liver RNA was extracted using the Qiagen RNeasy Plus Mini Kit and sample quality confirmed by Bioanalyzer
mRNA libraries constructed with NEBNext Ultra RNA Library Prep Kit for Illumina. Size selection was perfomed using the AMPure XP system followed by analysis of library purity.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ctrl_B2D_fpkm.txt
|
| Data processing |
Sequences were mapped to the mm10 UCSC reference genome using STAR.
RPKM values were calcualted using FeatureCounts
DESeq2 was used to calculate differentially expressed genes with p values adjusted using the Benjamini and Hochberg's method for controlling false discovery rate (FDR)
Genes with significant differential expression were determined by p<0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files including FPKM for Ctrl vs. B2-Deficient (Ctrl_B2D_fpkm.txt)
Supplementary files format and content: tab-delimited text files including FPKM for Ctrl + Fenofibrate vs. B2-Deficient + Fenofibrate (CtrlFF_B2DFF_fpkm.txt)
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Jun 18, 2022 |
| Contact name |
Peter Masschelin |
| E-mail(s) |
masschel@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE206200 |
Vitamin B2 enables PPARa regulation of fasting glucose availability |
|
| Relations |
| BioSample |
SAMN29096000 |
| SRA |
SRX15713708 |
