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Series GSE135399 Query DataSets for GSE135399
Status Public on May 25, 2020
Title Modelling rostro-caudal neural tube regionalization from human embryonic stem cells with a microfluidic morphogenic gradient
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Studies in animal models have been fundamental for understanding brain development but only a fraction of these findings have been validated in a human context. Here, we tissue-engineered a model (MiSTR) of human neural tube regionalization based on human embryonic stem cells (hESCs) and microfluidic cell culturing. By exposing differentiating hESCs to a WNT signalling gradient we mimicked early rostro-caudal neural patterning, and with >80% reproducibility generated a coherent tissue with progressive caudalization from forebrain over midbrain to hindbrain, including formation of isthmic organiser characteristics. Single-cell transcriptomics revealed that rostro-caudal organization was established already at 24 hours of differentiation, before expression of neural markers. Moreover, the transcriptomic hallmarks of rostro-caudal MiSTR organization accurately recapitulated gene expression patterns of the early rostro-caudal neural plate in mouse embryos. MiSTR thereby represents a novel in vitro model of human neurodevelopment to deconstruct and systematically analyze factors responsible for rostro-caudal neural tube patterning.
Overall design Single-cell transcriptomics of an in vitro model of early human neural patterning, at various time points and dorsal and ventral locations.
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Contributor(s) Rifes P, Isaksson M, Rathore GS, kirk PA, Møller OK, Barzaghi G, Lee J, Egerod KL, Rausch DM, Parmar M, Pers TH, Laurell T, Kirkeby A
Citation(s) 32451506
Submission date Aug 05, 2019
Last update date Jun 04, 2020
Contact name Gaurav Singh Rathore
Phone 50175653
Organization name University of Copenhagen
Department Department of Neuroscience
Lab Agnete Kirkeby lab
Street address Department of Neuroscience Faculty of Health and Medical Sciences Blegdamsvej 3B, Building 7, 4th floor
City Copenhagen
ZIP/Postal code 2200
Country Denmark
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (10)
GSM4007637 Day 0 Embryonic Stem cells (H9)
GSM4007638 Day 1 Dorsal Patterned cells
GSM4007639 Day 1 Ventral Patterned cells
BioProject PRJNA558753
SRA SRP217591

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Supplementary file Size Download File type/resource
GSE135399_RAW.tar 640.3 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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