|
| Status |
Public on Aug 10, 2023 |
| Title |
Mouse embyronic stem cells in 3D cell culture |
| Sample type |
RNA |
| |
|
| Source name |
mESC, 72 h after 3D culture
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Sv+C/+P
cell type: Embryonic stem cell
cell line: CRL-1934
culture condition: 3D
|
| Treatment protocol |
3D culture condition: 10cm culture dishes were coated with 1% agarose to prevent cell adhesion and seeded 10^6 cells /agarose coated dish for 3 days.
|
| Growth protocol |
mESC are cultured in DMEM with 10% FBS, 10^3 U/mL LIF, 100µM NEAA, 1mM sodium pyruvate, 2mM L-glutamine, 71.4µM b-mercaptoethanol, 100 U/ml antibiotics. Cells were sub-cultured at the dilution of 1:10 to 1:20 at 80-90% confluence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Inclusion of 1 U/ µL of the RiboLock RNase Inhibitor (Thermo) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with RQ1 RNase-Free DNasee (Peomega) to remove trace amounts of genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with Mouse Gene 2.0 ST Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix).
|
| Description |
mESC-3D
|
| Data processing |
The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Chia-Chi Chang |
| E-mail(s) |
cjk31714@hotmail.com
|
| Organization name |
National Health Research Institutes
|
| Department |
Institute of Cellular and System Medicine
|
| Street address |
35 Keyan Road
|
| City |
Zhunan, Miaoli County |
| ZIP/Postal code |
35053 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE99942 |
Comparative study of 3D vs. 2D cell culture transcriptional changes of murine embryonic stem cells, stromal cells and lung cancer cells |
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