|
| Status |
Public on Aug 10, 2018 |
| Title |
RA patterned neural crest cells rep1 |
| Sample type |
RNA |
| |
|
| Source name |
hPSCs differentiated into the different anterior posterior populations at different time points as stated.
|
| Organism |
Homo sapiens |
| Characteristics |
patient group: RA patterned neural crest cells
|
| Treatment protocol |
H9:SOX10 hPSCs were differentiated into neural crest cells and samples taken along timepoints of differentiation corresponding to neural plate border progenitor cell state or migratory neural crest cells. We utilised protocols to generate cells along the anterior posterior axis. First using all-trans retinoic acid, to mimic previous protocols to posteriorise cranial neural crest cells (CD6 for cranial and VD6 for RA patterned cells). We also compared these to neural crest cells derived from Neuromesodermal progenitors, that are present in the primitive streak and give rise to the posterior neural and mesodermal tissues. We compared these populations (TD6- trunk neural plate border cells; TD9- trunk migratory neural crest cells) to determine which showed more posterior gene expression patterns and assess determine any novel markers of hPSC derived neural crest cell populations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction according to manufacturers' instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylation of sense DNA fragments carried out according to Affymetrix protocol
|
| |
|
| Hybridization protocol |
5.2µg of fragmented and biotinylated DNA molecules were applied to the Human Clariom D GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
|
| Scan protocol |
Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols
|
| Description |
Differentiated H9:SOX10 hPSCs
|
| Data processing |
Data were analysed using the Affymetrix TAC software
|
| |
|
| Submission date |
Jan 16, 2018 |
| Last update date |
Aug 11, 2018 |
| Contact name |
Paul Roy Heath |
| E-mail(s) |
p.heath@sheffield.ac.uk
|
| Phone |
+44 114 2222254
|
| Organization name |
University of Sheffield
|
| Department |
Academic Neurology Unit
|
| Lab |
Heath
|
| Street address |
SITraN, 385a Glossop Road
|
| City |
Sheffield |
| State/province |
S. Yorks |
| ZIP/Postal code |
S10 2HQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE109267 |
Axial progenitors generate trunk neural crest cells in vitro |
|
