|
| Status |
Public on May 24, 2023 |
| Title |
Cocoa butter diet, Wild Type, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
diet: Cocoa butter
knockout status: WT
|
| Growth protocol |
Wild type C57b/6 mice were fed with 10% LFD, 45% HFD with saturated fatty acids, 45% HFD with n-3 fatty acids for 4-6 months. E-FABP knockout mice were fed with 45% HFD with saturated fatty acids, 45% HFD with n-3 fatty acids for 4-6 months. Skin RNA (n=3/group) from above groups (total 15 samples) was extracted for RNA sequencing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from the skin of mice using the Qiagen mRNA extraction kit, per the manufacturer's instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina Cat# 20020594), TruSeq RNA Single Indexes Set A (Illumina Cat# 20020492) and Set B (Illumina Cat # 20020493) per the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HFTWT_2
|
| Data processing |
Basecalling was performed in BaseSpace using bcl2fastq.
Sequences were directly aligned to the mouse mm10 reference genome assembly using tophat2 (version 2.0.13). The Ensembl GRCm38 v84 gtf was used to guide transcript expression.
Differential expression analysis between pairwise conditions was performed using the Tuxedo Suite program cuffdiff2 (version 2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: cuffnorm normalized FPKM values
|
| |
|
| Submission date |
Nov 11, 2020 |
| Last update date |
May 24, 2023 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE161296 |
High fat diets rich in fish oil promote hair loss via epidermal fatty acid binding-mediated immunoregulation |
|
| Relations |
| BioSample |
SAMN16770590 |
| SRA |
SRX9486567 |
