|
| Status |
Public on Sep 23, 2024 |
| Title |
MSC_NSC_2_24 h (transcriptome) |
| Sample type |
RNA |
| |
|
| Source name |
human bone marrow-derived MSCs , 24h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human bone marrow-derived MSCs
timepoint: 24h
replicate: R2
treatment: neurogenic differentiation medium
|
| Treatment protocol |
Time-course cell samples were collected at 0, 3, 6, 9, 12, 24 and 48 h after addition of a standard commercial neurogenic differentiation medium (C-28015, PromoCell).
|
| Growth protocol |
Cells were seeded at a density of 100.000 per 25 cm2 flask (coated with fibronectin), grown with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1-2 passages before induction of the trans-differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeling of cRNA was performed following the instructions from Low Input Quick Amp Labeling Kit (One-Color) (Agilent Technologies, Santa Clara, CA, USA). The cRNA samples were using RNeasy Mini Kit (Qiagen, Hilden, Germany). Resulting cRNA concentrations were determined using a NanoDrop™ 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).
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| |
|
| Hybridization protocol |
The labeled cRNA samples were hybridized to Human SurePrint G3 Gene Expression Microarrays (V3, G4851C) from Agilent Technologies following the inctructions from the Gene Expression Hybridization Kit (Agilent Technologies)
|
| Scan protocol |
The microarray slides were scanned with a resolution of 3 μm.
|
| Data processing |
Raw data was extracted using Feature Extraction software (Agilent Technologies, Santa Clara, CA, USA). Raw microarray data were extracted and concatenated into one matrix using python (v 3.7) with numpy (v 1.16.4).
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Annika Engel |
| E-mail(s) |
[email protected]
|
| Organization name |
Saarland University
|
| Department |
Center for Bioinformatics
|
| Lab |
Chair for Clinical Bioinformatics
|
| Street address |
Campus E2 1
|
| City |
Saarbrücken |
| State/province |
Saarland |
| ZIP/Postal code |
66123 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21185 |
| Series (2) |
| GSE253566 |
Paving the way to a neural fate - RNA signatures in naive and trans-differentiating Mesenchymal Stem Cells - transcriptome data |
| GSE253567 |
Paving the way to a neural fate - RNA signatures in naive and trans-differentiating Mesenchymal Stem Cells |
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