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. Author manuscript; available in PMC: 2015 Feb 1.
Published in final edited form as: Trends Mol Med. 2013 Dec 24;20(2):91–104. doi: 10.1016/j.molmed.2013.11.004

Table 2.

Gene expression data of iPSCs and derived neurons. a,b

Original phenotype/Disease GSE # Source Tissue Target Tissue iPSC reprogramming Gene expression data Platform Ref
Timothy syndrome 25542 Fibroblasts Cortical neurons (glutamatergic, GABAergic) Retroviral

  1. Fibroblasts

  2. iPSCs

  3. iPSC-derived neurospheres (day 7)

  4. iPSC-derives neurons at rest (day 45)

  5. iPSC-derived neurons kept in KCl

  6. ESCs

  7. ESC-derived neurospheres

  8. ESC-derived neurons at rest

 Illumina HumanRef-8 v3.0 expression beadchip [22]
Rett syndrome 21037 Fibroblasts Cortical neurons (GABAergic, glutamatergic) Retroviral

  1. Fibroblasts

  2. iPSCs

  3. ESCs

 Affymetrix Human Gene 1.0 ST Array [13]
BCKDK mutation 39447 Fibroblasts Tuj1+/Map2+ neurons Episomal

  1. Fibroblasts

  2. iPSCs

  3. iPSC-derived neural progenitors

  4. iPSC-derived neurons

 Nimblegen Homo sapiens HG18 Expression Array [92]
Schizophrenia 25673 Fibroblasts Glutamatergic (most, ~60%) GABAergic (30%) Dopaminergic (<10%) Lentiviral

  1. iPSC-derived neurons (6weeks old)

 Affymetrix Human Gene 1.0 ST Array [86]
26629 Skin fibroblasts, liver fibroblasts Glutamatergic neurons Retroviral

  1. iPSCs

  2. iPSC-derived neurons (day 10)

  3. iPSC-derived neurons (day 32)

 Affymetrix Human Gene 1.0 ST Array [87]
NRXN1 knockdown - Fibroblasts Neural stem cells, Tuj1+ neurons, astrocytes, oligodendrocytes PiggyBac transposon

  1. iPS-derived neural stem cells (0 weeks)

  2. iPS-derived neural stem cells (4 weeks)

 Illumina HiSeq 2000 [83]
Additional studies (no defined phenotype) 32625 Fibroblasts Glutamatergic neurons Retroviral

  1. iPSCs

  2. iPSC-derived neurons

 Illumina HiSeq 2000 [107]
41565 Fibroblasts Cortical neurons: early forebrain neurons, glia, glutamatergic, GABAergic Retroviral

  1. iPSCs

  2. ESCs

  3. iPSC-derived neurons (50 days)

 Illumina HumanHT-12 V4.0 expression beadchip [72]
a

Abbreviations: iPSCs, induced pluripotent stem cells; BCKDK, branched chain ketoacid dehydrogenase kinase; ESCs, embryonic stem cells; GEO, Gene Expression Omnibus; GSE, GEO series; KCl, potassium chloride; NRXN, neurexin.

b

We have excluded the transcriptomic data from iPSC-derived neurons from Parkinson’s, Alzheimer’s, spinal muscular atrophy fronto-temporal dementia and other neurological disorders despite its existence in the database, to focus on neurodevelopmental space.