|
| Status |
Public on Jan 25, 2018 |
| Title |
RIC_r1 |
| Sample type |
RNA |
| |
|
| Source name |
Ribosome-induced cell clusters (RICs) replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal fibroblast
|
| Treatment protocol |
Cells were collected using conventional trypsin digestion. The obtained cell suspensions were adjusted to approximately 2.5 × 105 cells/mL in PluriSTEM Human ES/iPS Medium (Merck) and then applied 2 ml to 6-well plate (Thermo Fisher Scientific) containing 20 µl of ribosome solution (1 µg /µl) that is extracted from Lactobacillus acidophillus. The plated cells were cultured for 14 days, with half the medium replaced every 3 or 4 days.
|
| Growth protocol |
HDFs purchased from Cell Applications were used within 3 passages from culturing of a new vial. HDFs were maintained at 37°C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used the TRIzol reagent (Thermo Fisher Scientific) with 1.0-mm glass beads (WAKENBTECH), a KONTES Homogenizer pestle (Kimble Chase), and a ReliaPrep RNA Cell Miniprep System (Promega) for purification. RNA quality was assessed using a Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
To generate Cy3-labeled cRNA, total RNA (150 ng) was reverse-transcribed using a Low Input Quick Amp Labeling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
The cRNA was fragmented and subsequently hybridized to the SurePrint G3 Human Gene Expression 8×60K v2 chip (Agilent Technologies) according to the manufacturer’s protocol, with 3 technical replicates used for each cell type.
|
| Scan protocol |
Microarray chips were scanned using a DNA Microarray Scanner (Agilent Technologies). Microarray data were feature-extracted using Agilent Feature Extraction software version 11.5.1.1.
|
| Description |
Gene expression of ribosome-induced cell clusters (RICs) replicate 1
|
| Data processing |
Microarray intensities were intra- and inter-array normalized using Limma package version 3.14.4 in the R statistical computing environment. Signal intensities for non-unique probe names were averaged.
|
| |
|
| Submission date |
May 18, 2017 |
| Last update date |
Jan 26, 2018 |
| Contact name |
Yutaka Saito |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Advanced Industrial Science and Technology (AIST)
|
| Street address |
2-4-7 Aomi
|
| City |
Koto-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
135-0064 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE99053 |
Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency [Array] |
| GSE99089 |
Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency |
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