Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

(2015) Jessica Mariani et al.   CELL

Developmental regulation of tau splicing is disrupted in stem cell-derived neurons from frontotemporal dementia patients with the 10 + 16 splice-site mutation in MAPT

(2015) Teresa Sposito et al.   HUMAN MOLECULAR GENETICS

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

(2015) Anca M Paşca et al.   NATURE METHODS

The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex

(2015) Erin Knock et al.   Neural Development

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Human stem cell models of dementia

(2014) F. J. Livesey   HUMAN MOLECULAR GENETICS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

(2014) Joyce van de Leemput et al.   NEURON

Patches of Disorganization in the Neocortex of Children with Autism

(2014) Rich Stoner et al.   NEW ENGLAND JOURNAL OF MEDICINE

Physiological Characterisation of Human iPS-Derived Dopaminergic Neurons

(2014) Elizabeth M. Hartfield et al.   PLoS One

Generation of Rejuvenated Antigen-Specific T Cells by Reprogramming to Pluripotency and Redifferentiation

(2013) Toshinobu Nishimura et al.   Cell Stem Cell

In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue

(2013) Brooke E. Hjelm et al.   HUMAN MOLECULAR GENETICS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Remodeling Neurodegeneration: Somatic Cell Reprogramming-Based Models of Adult Neurological Disorders

(2013) Liang Qiang et al.   NEURON

Pyramidal Neurons Derived from Human Pluripotent Stem Cells Integrate Efficiently into Mouse Brain Circuits In Vivo

(2013) Ira Espuny-Camacho et al.   NEURON

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

(2012) Hongkui Zeng et al.   CELL

Delayed Maturation and Differentiation of Neurons in Focal Cortical Dysplasia With the Transmantle Sign: Analysis of Layer-Specific Marker Expression

(2012) Takafumi Sakakibara et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

RT-qPCR work-flow for single-cell data analysis

(2012) Anders Ståhlberg et al.   METHODS

Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells

(2012) Mason A. Israel et al.   NATURE

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses

(2012) Yichen Shi et al.   NATURE NEUROSCIENCE

Passaging and colony expansion of human pluripotent stem cells by enzyme-free dissociation in chemically defined culture conditions

(2012) Jeanette Beers et al.   Nature Protocols

Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks

(2012) Yichen Shi et al.   Nature Protocols

Modeling human cortical development in vitro using induced pluripotent stem cells

(2012) J. Mariani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling familial Alzheimer's disease with induced pluripotent stem cells

(2011) Takuya Yagi et al.   HUMAN MOLECULAR GENETICS

Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

(2011) Sergiu P Paşca et al.   NATURE MEDICINE

A bioinformatic assay for pluripotency in human cells

(2011) Franz-Josef Müller et al.   NATURE METHODS

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

Neocortical Layer Formation of Human Developing Brains and Lissencephalies: Consideration of Layer-Specific Marker Expression

(2010) Takashi Saito et al.   CEREBRAL CORTEX

Development of Defective and Persistent Sendai Virus Vector

(2010) Ken Nishimura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols