|
| Status |
Public on Jan 09, 2024 |
| Title |
RNAseq_cDiet_Ing_dNT_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Epididymal (eWAT)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Epididymal (eWAT)
genotype: Dido1_dNT mutant
strain: C57BL/6
|
| Treatment protocol |
Mice were maintained at 22º on a normal diet (ND) (SAFE150) composed of 12.6% fat, on a 12/12-h light/dark cycle with ad libitum access to food and water. A control diet (CD) / high fat diet (HFD) pair, was used as recommended by manufacturer. CD (Ssniff E15748) composed of 4.1% fat. HFD (Ssniff E15744) composed of 45% fat was used to induce obesity.
|
| Growth protocol |
Mixed genetic background dNT mice were generated as described (Fütterer, et al., 2005; doi:10.1172/JCI24177) and backcrossed more than 10 times on a C57BL/6 background.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified with the Split RNA Extraction Kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for inguinal WAT were prepared by BGI Genomics (China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
White Adipose Tissue (WAT)
|
| Data processing |
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
The expression level of all genes was estimated by DESeq2 1.40.1 in RStudio 2023.03.1+446
Assembly: GRCm38/mm10 assembly
Supplementary files format and content: tab-delimited text files include cov, FPKM, and TPM values for each Sample (*.gtf)
Supplementary files format and content: Matrix table with TPM values for every transcript and every sample (*.csv)
|
| |
|
| Submission date |
Jun 28, 2023 |
| Last update date |
Jan 09, 2024 |
| Contact name |
Tirso Pons |
| E-mail(s) |
tpons@cnb.csic.es
|
| Organization name |
Centro Nacional de Biotecnologia
|
| Department |
Inmunology and Oncology
|
| Lab |
411
|
| Street address |
C/ Darwin 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28043 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE236034 |
DIDO is necessary for the adipogenesis that promotes diet-induced obesity [II] |
| GSE236036 |
DIDO is necessary for the adipogenesis that promotes diet-induced obesity |
|
| Relations |
| BioSample |
SAMN36027529 |
| SRA |
SRX20809992 |
