|
| Status |
Public on Jun 07, 2016 |
| Title |
p53-/- MEFs, Forskolin, Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Murine embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype/variation: p53-/-
cell type: Murine embryonic fibroblasts
treatment: Forskolin
|
| Treatment protocol |
Two days past confluence 3T3-L1 preadipocytes or MEFs were treated with P6 (500 nM) or vehicle (DMSO) for 15 minutes before stimulated with forskolin (10 uM) or vehicle (DMSO). RNA was harvested after 1 hour of stimulation. Chromatin was harvested in 3T3-L1 preadipocytes 15 minutes after forskolin stimulation.
|
| Growth protocol |
3T3-L1 preadipocytes were maintained in DMEM supplemented with 10% calf serum with 2 mM L-glutamin and 100 U/ml Pen-Strep. MEFs were maintained in DMEM supplemented with 10% fetal bovine serum with 2 mM L-glutamin and 100 U/ml Pen-Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.
Purified RNA was subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of CRTC2 enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.
|
| Data processing |
Aligment to mm9 using STAR
Differential gene expression identified using DESeq
CRTC2 ChIP-seq binding sites identified using HOMER
Differential CRTC2 binding identified using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Jun 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
|
| Phone |
+45 6550 2340
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE82282 |
MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3 |
|
| Relations |
| BioSample |
SAMN05208868 |
| SRA |
SRX1822316 |
