|
| Status |
Public on Aug 24, 2021 |
| Title |
mA-3T3L1-LACZ-replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
mature 3T3-L1 adipocytes
|
| Organism |
Mus musculus |
| Characteristics |
genotype: LacZ Adenovirus (control)
strain: C57BL/6
age: 3T3-L1 cells were induced to differentiate into matutre adipocytes fr a period of 7 days after which cell were infected with Adenovirus (LacZ)
|
| Treatment protocol |
3T3-L1 adipocytes were infected with 100 pfu/cell on day 7 of differentiation. Experiments were performed 3 days after adenoviral transduction.
|
| Growth protocol |
At 2 days post-confluency 3T3-L1 cells were treated with a differentiation cocktail containing: DMEM, 10% CS, insulin (870 nM), TZD (5µM), Dex (1 µM), and IBMX (500 µM). On day 3 of differentiation, cells were switched to differentiation cocktail excluding IBMX and Dex for remaining duration of differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using Qiagen Rneasy mini kit according to the manufacturers protocol
Library preparation and RNA-Seq was carried out by the Core facility Genomics, Medical University of Vienna, Vienna, Austria. Briefly, sequencing libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer’s instructions and sequenced on a Illumina NextSeq500 platform in a 75bp single-read mode
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq generation, bcl2fastq via Basespace
alignment and extraction of counts/gene, STAR aligner (STAR_2.5.0b) via Basespace,
differential gene expression analysis, DESeq2 (1.6.3) via Basespace
Genome_build: UCSC mm10
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample
|
| |
|
| Submission date |
Aug 06, 2020 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Markus Jeitler |
| E-mail(s) |
markus.jeitler@meduniwien.ac.at
|
| Organization name |
Medical University Vienna
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
A-1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE139163 |
LMO3 reprogramms viseral adipocyte metabolism during obesity |
| GSE155781 |
mouse 3T3L1 adipocytes transduced with Lmo3- or LacZ-Adenovirus |
|
| Relations |
| BioSample |
SAMN15746764 |
| SRA |
SRX8897026 |
