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Series GSE211660 Query DataSets for GSE211660
Status Public on Oct 16, 2023
Title Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma [Bulk RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Pediatric malignancies, including neuroblastoma, are best understood as disorders of development. Neuroblastoma explicitly represents a failure of sympathoadrenal development. Yet, its molecular pathogenesis remains elusive. The application of an in vitro model of human sympathoadrenal development would allow for studying the normal developmental trajectory. Such a model could also interrogate the early steps toward neuroblastoma transformation utilizing genetic manipulation. However, in vitro models have thus far been unable to generate the cells of interest reliably. We developed and characterized a human in vitro pluripotent stem cell-based model via sequential single-cell RNA sequencing throughout sympathoadrenal development. We demonstrate the power of our model to study early events of the development of human neuroblastoma. We do so by identifying the differences between normal and patient-specific induced pluripotent stem cells, derived from a child with familial neuroblastoma, harboring a germline mutation in the Anaplastic Lymphoma Kinase (ALK) gene.
 
Overall design Induced pluripotent stem cells (iPSC) were differentiated along the sympathoadrenergic precursor (SAP) development during a 40 day long differentiation process. We performed bulk RNA sequencing on selected time-points (D0/Start, D3, D7, D11, D16, D21, D23, D25, D27, D29, D31, D35, D40) covering the entire differentiation process. The experiments were repeated four times, twice with a human induced pluripotent stem cell line (J2) and twice with a human embryonic stem cell line (H9) for a total of four biological replicates.
Web link https://doi.org/10.1016/j.isci.2023.108096
 
Contributor(s) Van Haver S, Speleman F, Roberts SS
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Submission date Aug 19, 2022
Last update date Oct 17, 2023
Contact name Sarah-Lee Bekaert
E-mail(s) sarahlee.bekaert@ugent.be
Organization name UGent
Street address Corneel Heymanslaan 10
City Ghent
State/province No state
ZIP/Postal code 9000
Country Belgium
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (48)
GSM6482169 Normal SAP development Start, Bio_Rep3 , Bulk- RNAseq
GSM6482170 Normal SAP development D3, Bio_Rep3 , Bulk- RNAseq
GSM6482171 Normal SAP development D7, Bio_Rep3 , Bulk- RNAseq
This SubSeries is part of SuperSeries:
GSE211664 Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma
Relations
BioProject PRJNA871265

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE211660_RAW.tar 16.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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