|
| Status |
Public on Mar 26, 2017 |
| Title |
KD_d8_#2_13_(miRNA-3_0) |
| Sample type |
RNA |
| |
|
| Source name |
KD 12-days EBs second chip
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129
gender: male
genotype/variation: Strip2 silenced (KD)
cell type: embryoid bodies (EBs)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
WT ESCs, SCR ESCS and KD ESCs were differentiated applying the hanging drop protocol for 4-, 8-, 12- and 16-days (Wagh et al. Fam40b is required for lineage commitment of murine embryonic stem cells. Cell Death Dis 2014, 5: e1320). Total RNA from was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen
|
| Label |
biotin
|
| Label protocol |
700 ng total RNA was used as the starting material, and the Affymetrix FlashTag Biotin HSR RNA Labelling kit was used for miRNA ligation (Affymetrix, United Kingdom) according to the manufacturer’s instructions. The labeled samples were hybridized to the Affymetrix miRNA 3.0 arrays for 16 h at 48 °C in an Affymetrix hybridization oven 645
|
| |
|
| Hybridization protocol |
After incubation, the arrays were washed and stained in the fluidics station 450 using fluidics script FS450_0002
|
| Scan protocol |
Arrays were scanned using an Affymetrix Gene-Chip Scanner-3000-7G
|
| Description |
KD_d8_2_13_(miRNA-3_0)
|
| Data processing |
The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA). QC passed CEL files were further analyzed using the Bioconductor package limma . All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.
|
| |
|
| Submission date |
Mar 20, 2017 |
| Last update date |
Mar 26, 2017 |
| Contact name |
Agapios Sachinidis |
| E-mail(s) |
a.sachinidis@uni-koeln.de
|
| Phone |
+492214787373
|
| Organization name |
University of Cologne
|
| Department |
Institute of Neurophysiology
|
| Street address |
Robert-Kochstr. 39
|
| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16384 |
| Series (2) |
| GSE96808 |
Genome-wide profiling of miRNAs during differentiation of wild (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs, and Strip2 silenced (KD) ESCs |
| GSE96809 |
Genome-wide profiling of genes and miRNAs during differentiation of wild (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs, and Strip2 silenced (KD) ESCs |
|
