|
| Status |
Public on Jul 23, 2021 |
| Title |
HFD_het2 |
| Sample type |
SRA |
| |
|
| Source name |
WAT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Mof heterozygous
diet: high fat diet
|
| Treatment protocol |
Animals was kept in standart diet (SD) or high fat diet (HFD)
|
| Growth protocol |
Tissue was extract directly from the animals
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
WAT was weighed and an equal amount of tissue was used to extract mRNA from WAT. For RNA extraction from various sources were lysed directly in TRIZOL and samples were homogenized using an electric tissue homogenizer. Then, samples were incubated with 95% EtOH and transferred into mini-kit RNA extraction Zymo kit (R1054) and pure total RNA was extracted according to the manufacturer’s instructions. RNA concentrations were quantified on a Qubit 2.0 Fluorometer (Life Technology) and quality for deep sequencing checked by Fragment analyzer.
After quality control was then used to generate libraries using Illumina TruSeq RNA Sample Prep v2 (RS-122-2001). The manufacturer’s recommendations were followed and the libraries were sequenced on an Illumina NovaSeq6000 sequencer. All sequence data were performed in 3 biological replicates for SD group and duplicates for HFD group. The reads were conducted at 2 x 100 bp length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads for mouse bulk RNA-seq datasets were mapped with following the default SnakePipes parameters of bulk RNAseq pipeline (Bhardwaj et al. 2019). In brief, STAR software alignment against mouse genome version GRCm38. The total number of sequenced reads averaged 15 million pairs of which mean alignment of 65 % of the reads were uniquely mapped. Reads were counted with featureCounts (subread-1.5.0-p1). Differential expression analysis was performed with DESEQ2 (v1.26). Multi-FASTA QC statistics indicated data were of high quality and sequencing depth was sufficient to test for differential expression between conditions. Differential genes were called with an FDR threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts
|
| |
|
| Submission date |
Jul 23, 2020 |
| Last update date |
Jul 23, 2021 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE154967 |
MOF haploinsufficiency triggers diet-induced obesity resistance (RNA-seq) |
| GSE156463 |
MOF haploinsufficiency triggers diet-induced obesity resistance |
|
| Relations |
| BioSample |
SAMN15618164 |
| SRA |
SRX8806140 |
