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Sample GSM2936313 Query DataSets for GSM2936313
Status Public on Aug 10, 2018
Title Trunk neural crest precursors rep2
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: Trunk neural crest precursors
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

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
TC0100006432.hg.1 3.817079
TC0100006433.hg.1 3.780454
TC0100006434.hg.1 5.522651
TC0100006435.hg.1 2.916913
TC0100006436.hg.1 3.066331
TC0100006437.hg.1 3.818051
TC0100006438.hg.1 7.294701
TC0100006439.hg.1 4.552825
TC0100006440.hg.1 2.674557
TC0100006441.hg.1 5.752835
TC0100006442.hg.1 4.580481
TC0100006443.hg.1 4.920071
TC0100006444.hg.1 4.366745
TC0100006445.hg.1 4.377142
TC0100006446.hg.1 3.576862
TC0100006447.hg.1 16.38913
TC0100006448.hg.1 5.555282
TC0100006449.hg.1 3.300405
TC0100006450.hg.1 3.752716
TC0100006451.hg.1 4.505675

Total number of rows: 138745

Table truncated, full table size 3668 Kbytes.




Supplementary file Size Download File type/resource
GSM2936313_13_TA_2.6_Clariom_D_Human_.CEL.gz 24.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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