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Status |
Public on Mar 26, 2017 |
Title |
WT_ES_2 |
Sample type |
RNA |
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Source name |
WT ESCs second chip
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Organism |
Mus musculus |
Characteristics |
strain: 129 gender: male genotype/variation: wild type cell type: embryonic stem cells (ESCs)
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Treatment 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 the undifferentiated and 4-, 8-, 12- and 16-day EBs was isolated and gene expression was analyzed by the Affymetrix (Mouse430 2.0) chip.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from the was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen
|
Label |
biotin
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Label protocol |
100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer
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Hybridization protocol |
12.5µg of fragmented aRNA was hybridized to the Mouse Genome 430 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.
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Scan protocol |
Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions
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Data processing |
The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.
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Submission date |
Mar 20, 2017 |
Last update date |
Mar 26, 2017 |
Contact name |
Agapios Sachinidis |
E-mail(s) |
a.sachinidis@uni-koeln.de
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Phone |
+492214787373
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Organization name |
University of Cologne
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Department |
Institute of Neurophysiology
|
Street address |
Robert-Kochstr. 39
|
City |
Cologne |
State/province |
NRW |
ZIP/Postal code |
50931 |
Country |
Germany |
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Platform ID |
GPL1261 |
Series (2) |
GSE96807 |
Genome-wide profiling of genes 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 |
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