|
| Status |
Public on Jul 20, 2024 |
| Title |
Organoid D120 D120_02 |
| Sample type |
RNA |
| |
|
| Source name |
LMNSC01 neural stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
culture time (days): 120
number of organoids: 1
experimental run: 3
culture medium, o2 concentration (%): Neurocult Proliferation medium, 4% O2 environment
|
| Treatment protocol |
Neurocult Proliferation medium 4% oxygen, Neurocult differntiation medium 20% oxygen, BrainPhys medium 4% oxygen.
|
| Growth protocol |
Organoids generated in vitro initiated with neural stem cell line LMNSC01 (previously referred to as LM-NSC008) with 1000 cells per 6 µL matrigel cultured under hypoxia (4% O2) in NeuroCult Proliferation media (NC.Prol) and harvested at 6 time points
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted using the miRNeasy mini kit (HB-1277-066,Qiagen). Concentration was assessed by Nanodrop spectrophotometer ND-1000 and Qubit 3.0 Fluorometer , with mRNA fragmentation and quality assessed by 2100 Bioanalyzer
|
| Label |
n/a
|
| Label protocol |
We utilized the NanoString Neuropathology Profiling panel, consisting of genes targeting six fundamental themes: neurotransmission, neuron-glia interactions, neuroplasticity, cell structure integrity, neuroinflammation, and metabolism
|
| |
|
| Hybridization protocol |
RNA was hybridized with the gene panel Codeset at 65 °C for 16 hr.
|
| Scan protocol |
The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, with subsequent data analysis performed using nSolver.
|
| Description |
Organoid D120
Bulk RNAseq, Neuropathology panel
|
| Data processing |
Raw data was first normalized to internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Gene expression variability of less than 20% within a single organoid was the criterion for acceptance.
|
| |
|
| Submission date |
Jul 19, 2024 |
| Last update date |
Jul 20, 2024 |
| Contact name |
Yate-Ching Yuan |
| E-mail(s) |
yyuan@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 East Duarte
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL34724 |
| Series (1) |
| GSE272682 |
Organoids directly derived from L-MYC immortalized human neural stem cells (LMNSC01) model cerebral development in vitro |
|
