|
| Status |
Public on Nov 30, 2017 |
| Title |
KO_Regular Diet_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
KO_Regular Diet
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Nrf1 KO
treatment: Regular diet
tissue: Liver
replicate: 2
|
| Treatment protocol |
WT and Nrf1 KO mice were fed regular diet (RD) or 1 week with high cholesterol diet (CholD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. mRNA enriched libraries were prepared using Directional RNA-Seq Wafergen.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA was enriched from total RNA for library prep
|
| Data processing |
Using the Illumina HiSeq 2500, Real Time Analysis provided basecalling.
Sequenced reads were mapped to mm10 whole genome using TopHat version 8.7.
Accepted read Bam files were sorted using Picard SortSam.
Sorted Bam files were input for transcript assembly using Cufflinks version 7 for individual samples, and the complete transcript assembly for differential analysis was done generated using Cuffmerge version 3.
CuffDiff version 7 was used for differential expression analysis. Transcript abundance was reported as Fragment reads Per Kilobase of exon per Megabase of library size (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include average FPKM values, relative differences, and statistical signficance, reported as p-value and false discovery rate (q)
|
| |
|
| Submission date |
Sep 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott Widenmaier |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard TH Chan School of Public Health
|
| Department |
Genetics and Complex Diseases
|
| Lab |
Hotamisligil Lab
|
| Street address |
665 Huntington Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE103949 |
Next Generation Sequencing for Quantitative Expression Analysis of Wild Type and Nrf1 deficient Liver Transcriptomes from Regular Diet (RD) or High Cholesterol Diet (CholD) fed mice |
|
| Relations |
| BioSample |
SAMN07662829 |
| SRA |
SRX3195751 |
