|
| Status |
Public on Feb 20, 2017 |
| Title |
KO_ESC_Sample2 |
| Sample type |
RNA |
| |
|
| Source name |
Sirt1-knock-out ESC
|
| Organism |
Mus musculus |
| Characteristics |
strain: (129X1 x 129S1)F1
genotype: Sirt1-/-
|
| Treatment protocol |
Both ESC cells were maintained under 0.1% gelatin coated tissue culture dish
|
| Growth protocol |
Wild-type and Sirt1 deficient murine R1 ESCs were grown in DMEM-high glucose medium supplemented with 2 mM L-glutamine, 20 mM HEPES, MEM non-essential amino-acid, penicillin/streptomycin solution, 0.1 mM beta-mercaptoethanol, 15% heat-inactivated FBS, and 100 IU/ml ESGRO/LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from Sirt1+/+ or Sirt1-/- ESCs was isolated using the RNeasy Mini Kit (Qiagen Inc) including treatment of DNase I (Qiagen Inc).
|
| Label |
Biotin
|
| Label protocol |
100 ng of total RNA isolated from Sirt1+/+ or Sirt1-/- ESCs were converted to cDNA, followed by biotin-labeled using GeneChip 3’ in vitro transcription (IVT) kit
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
|
| Description |
Gene expression data from Sirt1 knock-out ESCs
|
| Data processing |
The CEL files for 6 cell samples (3 samples for each genotype ESC) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing Sirt1+/+ versus Sirt1-/- ESCs.
|
| |
|
| Submission date |
Aug 18, 2014 |
| Last update date |
Feb 20, 2017 |
| Contact name |
DONG-MYUNG SHIN |
| E-mail(s) |
[email protected]
|
| Phone |
82-2-3010-2086
|
| Organization name |
University of Ulsan College of Medicine
|
| Department |
Department of Biomedical Sciences
|
| Street address |
Pungnap-2 dong, Songpa-gu
|
| City |
Seoul |
| ZIP/Postal code |
05505 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE60500 |
Genomewide gene expression analysis of murine Sirt1 wild-type or knock-out embryonic stem cells (ESCs) |
| GSE60639 |
Transcriptome_Methylome_Sirt1KOESC |
|
