|
| Status |
Public on Jun 11, 2018 |
| Title |
WAT_array_Ing1-KO_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
WAT_array_Ing1-KO
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
genotype: Ing1-/-
tissue: male gonadal White Adipose Tissue (WAT)
|
| Treatment protocol |
Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and wildtype (WT) animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gonadal WAT was individually collected from 9 male mice per genotype (59-67 day old) and snap-frozen in liquid nitrogen. Total RNA was extracted with Qiazol and an Ultra turrax homogeniser. RNA was further purified using the RNeasy mini kit with on-column DNase digest (Qiagen), quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer. Employing a sub-pooling approach (doi:10.1186/1471-2105-4-26), purified RNA from 3 animals of each genotype was pooled to create 3 biological replicates for microarray expression profiling.
|
| Label |
Cy3
|
| Label protocol |
Agilent one-color Quick Amp Labeling Kit following the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Agilent Hybridisation Oven and SurePrint G3 Mouse GE 8x60K microarrays following the manufacturer's protocol.
|
| Scan protocol |
Agilent Scanner G2505C with v.10.7.3.1 Feature Extraction Software at 3 µm resolution.
|
| Description |
Ing1 knockout WAT, replicate 3
|
| Data processing |
The raw array data were processed using the Bioconductor package limma v.3.26.9 (https://bioconductor.org/packages/release/bioc/html/limma.html) following the standard workflow for single-channel Agilent arrays (chapter 17.4 of the User’s Guide). Following normexp background correction and quantile inter-sample normalisation, the control and low-signal probes were filtered out, the replicate probes were averaged and the knockout samples were compared against the wildtype samples for differential gene expression (lmFit; eBayes).
log2 signal intensity from limma after background correction, quantile normalisation, removal of control and low-signal probes, and averaging of replicate probes
|
| |
|
| Submission date |
Jun 02, 2017 |
| Last update date |
Jun 11, 2018 |
| Contact name |
Emil Karaulanov |
| Organization name |
Institute of Molecular Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE99605 |
Gene expression changes in white adipose tissue from Ing1- and Gadd45a- single- or double-knockout mice |
| GSE99607 |
Impaired DNA demethylation of C/EBP sites causes premature aging |
|
