|
| Status |
Public on Jul 09, 2019 |
| Title |
Std 4 |
| Sample type |
SRA |
| |
|
| Source name |
Std_eWAT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6j
age: 8 weeks
genotype/variation: Wild-type
diet: standard (Std)
tissue: epididymal white adipose tissue (eWAT)
molecule subtype: rRNA depleted RNA
|
| Treatment protocol |
epididymal white adipose tissues (eWAT) were harvested from fasted mice and immediately snap frozen and stored at -80°C until total RNA extraction
|
| Growth protocol |
8-week-old mice were randomly assigned standard, HF/HS or HF/HS +AOF diet and were fed ad libitum with the respective diets for 180 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from eWAT with the RNeasy Lipid Tissue Mini kit (Qiagen) according to the manufacturer's instructions and included a DNAse treatment step . Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit.
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Std4_S8_L00*
|
| Data processing |
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking
|
| |
|
| Submission date |
Oct 02, 2018 |
| Last update date |
Jul 09, 2019 |
| Contact name |
Romain Boidot |
| E-mail(s) |
rboidot@cgfl.fr
|
| Organization name |
CGFL
|
| Lab |
Molecular Biology Unit
|
| Street address |
1, rue Pr Marion
|
| City |
Dijon |
| ZIP/Postal code |
21079 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE120748 |
Transcriptome analysis of mice adipose tissues |
|
| Relations |
| BioSample |
SAMN10161256 |
| SRA |
SRX4783461 |
