|
| Status |
Public on Jan 11, 2021 |
| Title |
d2_PY_5 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal C3H/10T1/2 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H/10T1/2-SAM
group: PY.d2
transfection: Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid
day of differentiation: d2
experiment: exp6
|
| Treatment protocol |
Transfection conditions: EV (Empty Vector plasmid, Control), P (Pparγ gRNA-plasmid only), PY (Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid). All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.
|
| Growth protocol |
Cell were differntiated by targeted over-expression of endogenous Pparγ (transfection with plasmids containing Pparγ-targeted guide RNA) and treated with 5uM Rosiglitazone on day 0 (48 hrs after tranfection) to promote adipogenesis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with RLT/β-Me and mRNA extracted using Rneasy spin columns (Quiagen) with DNAse treaamnet. mRNA concentrations were determined with nano-drop and RNA quality/integrity assessed using RNA 6000 Nano (Aligent Technology) chips.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.3a.
2) Gene read coverages were computed with featureCounts v1.5.2 using ENSEMBL mouse annotation release 92 (GRCm38.92)
3) Differential expression analysis was performed using edgeR v3.22.0 with "y ~ 0 + group + Experiment" design while filtering low read counts less than 2 CPM in at least 5 samples
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts
|
| |
|
| Submission date |
Apr 22, 2020 |
| Last update date |
Jan 11, 2021 |
| Contact name |
Ali Altintas |
| E-mail(s) |
[email protected]
|
| Organization name |
Copenhagen University
|
| Department |
NNF Center for Basic Metabolic Research
|
| Lab |
Integrative Physiology
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE149083 |
Remodeling of white fat during browning involves YBX1 to drive thermogenic commitment |
|
| Relations |
| BioSample |
SAMN14668102 |
| SRA |
SRX8154503 |
