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| Status |
Public on Jul 14, 2016 |
| Title |
Embryonic stem cells culture conditions support distinct ES cell states associated with specific developmental stages and cell types |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Identification of transcripts in murine embryonic stem (ES) cell lines growing under 3 different self-renewing conditions; GMEM + 10% FCS, N2B27 + 2i (1 μM PD032 and 3 μM CHIR99021) and knockout serum replacement (KOSR) medium (80% Knockout DMEM, 20% Knockout Serum Replacement). Under all conditions, ES cells were grown on gelatin-coated dishes and passaged by trypsinisation. ES cells were cultured in each condition for at least 3 passages prior to sample collection.
The aim of this array experiment is to identify significant differences in transcript levels of ES cells grown under different conditions. Differences of transcript levels from the different conditions should be consistent among the biological and technical replicates for each.
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| Overall design |
Unsorted ES cells were maintained in serum/LIF, 2i/LIF or KOSR/LIF. Samples were collected from 3 independent ES cell clones from the 129/Ola background; E14, HVJu5.1 and HVJu9.3 For 2i/LIF (Morgani et al., 2013). For the 2i/LIF condition, 5 samples were collected with 2 samples each for HVJu5.1 and HVJu9.3 cell lines, for serum/LIF and KOSR/LIF conditions, 1 sample was collected for each cell line. RNA was extracted from all replicate clones. Therefore each condition is represented at least as biological triplicates. RNA isolation was performed using Qiagen RNeasy kits according to the manufacturer's instructions. RNA pellets were resuspended in Nuclease Free Water (ambion) and RNA concentration was measured using the Nanodrop system. 260/280 values for all samples were in the range of 1.8-2.0 RNA quality was additionally assessed using the Agilent 2100 BioAnalyzer with all samples having a RIN of ≥9.7.
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| Contributor(s) |
Gonzalez JM, Morgani SM, Bonderup K, Abelchian S, Brakebusch C, Brickman JM |
| Citation(s) |
27509134 |
| Submission date |
Aug 27, 2015 |
| Last update date |
Oct 03, 2019 |
| Contact name |
Sophie M Morgani |
| E-mail(s) |
morganis@mskcc.org
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| Organization name |
Sloan Kettering Institute, MSKCC
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| Department |
Development Program
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| Lab |
Hadjantonakis Lab
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| Street address |
Rockefeller Research Labs, 430 E 67th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL10787 |
Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA294077 |
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