Transcriptomics

Dataset Information

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Time line RNAseq of iPSC-derived neurons from ASD and control subjects.


ABSTRACT: To comprehensively profile early neurodevelopmental alterations in individuals with ASD, we harnessed a time series approach to monitor patient-derived induced pluripotent stem cells (iPSCs) throughout the recapitulation of cortical development. This dataset consists of patient derived neurons that go through all consecutive developmental stages (NSC-derived neurons) as well as a comparative set of iPSC-iNs (neurons generated from the same patients that bypass early NSC-like stages using an Ngn2-transgene approach). For this, we first used fluorescence-activated cell sorting (FACS) to purify a homogeneous population of NSCs based on the expression of the cell-surface markers CD184+/CD271-/CD44-/CD24-/CD15+. To trace ASD and control neurons over time, we performed a series of retroviral lineage-tracing experiments to trace the progenies of dividing NSCs using a retroviral vector expressing a membrane-tagged enhanced green fluorescent protein (eGFP) (CAG::LckN-eGFP). As differentiating neurons express PSA-NCAM on the cell surface, we established a FACS-based protocol for purification of defined subpopulations of retrovirally labeled eGFP+/PSA-NCAM+ double-positive neurons after 2, 4, 7 and 14 days of differentiation. IPSCs were sorted based on the expression of SSEA-4 and TRA1-81 and maturing iPSC-iNs were collected at the indicated days after induction by sorting for eGFP (indicative for the Ngn2 transgene)- and PSA-NCAM-positive cells.

INSTRUMENT(S): Illumina HiSeq 2500, TruSeq Stranded mRNA Sample Prep Kit (Illumina), BD InFlux Cytometer (Becton-Dickinson), Cutadapt, STAR

ORGANISM(S): Homo sapiens  

SUBMITTER: Simon T Schafer   Fred H Gage  

PROVIDER: E-MTAB-6018 | ArrayExpress | 2019-01-07

SECONDARY ACCESSION(S): ERP091820

REPOSITORIES: ArrayExpress, ENA

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