|
| Status |
Public on May 08, 2014 |
| Title |
RNA-seq Scr exp2, 3T3-L1 D0 |
| Sample type |
SRA |
| |
|
| Source name |
3T3-L1 pre-adipocytes (D0)
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
differentiation stage: pre-adipocytes
time: 0 hr
treatment: Scr. Lentivirus expressing shRNA against a scrambled sequence
|
| Treatment protocol |
3T3-L1 pre-adipocytes (day 0) were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Cells were harvested four hours after induction.
|
| Growth protocol |
3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days post confluency (day 0), the cells were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified RNA was subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions.
|
| |
|
| 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 |
Sequence reads were mapped to the mouse genome (mm9) using Bowtie (Langmead et al., 2009, Genome biology, 10(3):R25). Mapped reads in exons were counted using HOMER (Heinz et al., 2010, Mol Cell, 38(4):576-89) and differentially expressed genes (adjusted P<0.05) were identified using DESeq (Anders and Huber, 2010, Genome Biology, 11(10):R106). Bedgraph files were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of DHS and cutcount profiles as well as expression data in the UCSC genome browser.
|
| |
|
| Submission date |
May 07, 2014 |
| 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) |
| GSE57415 |
Molecular architecture of transcription factor hotspots in early adipogenesis |
|
| Relations |
| BioSample |
SAMN02767372 |
| SRA |
SRX535271 |
