A cross-species proteomic map reveals neoteny of human synapse development

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=5fdff881&gene_symbol_exact_match=1&gene_symbol=dcx

DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ecf5e3b7&gene_symbol_exact_match=1&gene_symbol=satb2

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d81e4aeb&gene_symbol_exact_match=1&gene_symbol=dcx

Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=a9cc60aa&gene_symbol_exact_match=1&gene_symbol=xbp1

Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=08a3324d&gene_symbol_exact_match=1&gene_symbol=satb2

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ed9b7a4b&gene_symbol_exact_match=1&gene_symbol=satb2

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=4f83fe83&gene_symbol_exact_match=1&gene_symbol=xbp1

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=8300a245&gene_symbol_exact_match=1&gene_symbol=xbp1

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

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=474805c1&gene_symbol_exact_match=1&gene_symbol=dcx

Dissecting neural differentiation regulatory networks through epigenetic footprinting

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2cfae2bd&gene_symbol_exact_match=1&gene_symbol=dcx

Altered proliferation and networks in neural cells derived from idiopathic autistic individuals

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2765b443&gene_symbol_exact_match=1&gene_symbol=dcx

Genomic DISC1 Disruption in hiPSCs Alters Wnt Signaling and Neural Cell Fate

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=032b8713&gene_symbol_exact_match=1&gene_symbol=dcx

Spatial profiling of early primate gastrulation in utero

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=572ffa49&gene_symbol_exact_match=1&gene_symbol=dcx

Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a445a5fc&gene_symbol=dcx

Dissecting the molecular basis of human interneuron migration in forebrain assembloids from Timothy syndrome

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=bae433b5&gene_symbol=olig1

Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX

Cortical organoids model early brain development disrupted by 16p11.2 CNV in autism

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=300f7fec&gene_symbol=hopx

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=fae5f876&gene_symbol_exact_match=1&gene_symbol=dcx

Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=c215acc6&gene_symbol_exact_match=1&gene_symbol=dcx

Hs; MacMul; Chimp;Orangutan

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

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a613d976&gene_symbol=dcx

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

https://nemoanalytics.org/p?l=2cfae2bd&g=DCX

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX

Long Term Maturation of Human Cortical Organoids Matches Key Early Postnatal Transitions

Sergiu Pasca, Daniel Geschwind

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=acff3407&gene_symbol=dcx

A critical period of translational control during brain development at codon resolution

bulkRNAseq, riboSeq, Proteomics, tRNA QPCR

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2eb6fafb&gene_symbol_exact_match=1&gene_symbol=dcx

Induction of myelinating oligodendrocytes in human cortical spheroids

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=74b652f6&gene_symbol=dcx

Spatiotemporal transcriptomic divergence across human and macaque brain development

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=d416d7e8&gene_symbol=dcx

looks like we only have macaqe for this - where is chimp? is human just brainspan or is this and/or souza human data different?

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=31d0c38d&gene_symbol_exact_match=1&gene_symbol=dcx

Reliability of human 3D cortical organoid generation

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=7e146d6e&gene_symbol=dcx

Neuronal Defects in a Human Cellular Model of 22q11.2 Deletion Syndrome

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=b46d5f94&gene_symbol_exact_match=1&gene_symbol=dcx

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=408a33fc&gene_symbol=dcx

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=72656283&gene_symbol=dcx

Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=3c351341&gene_symbol_exact_match=1&gene_symbol=dcx

Mm E18.5-P48, esp P1, P7, P21; marmoset P0-Y2

Atlas of the aging mouse brain reveals white matter as vulnerable foci

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=22a8db92&gene_symbol_exact_match=1&gene_symbol=dcx

Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=3618a37f&gene_symbol=dcx

Spatiotemporal proteomic atlas of multiple brain regions across early fetal to neonatal stages in cynomolgus monkey

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=f2ffb73b&gene_symbol_exact_match=1&gene_symbol=hopx

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=55679c3e&gene_symbol_exact_match=1&gene_symbol=dcn

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=7e14ad94&gene_symbol_exact_match=1&gene_symbol=satb2

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=f7d3dbfd&gene_symbol_exact_match=1&gene_symbol=dcn

Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=bcc3f487&gene_symbol_exact_match=1&gene_symbol=cux2

Molecular and spatial signatures of mouse brain aging at single-cell resolution

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=dacc1bf0&gene_symbol_exact_match=1&gene_symbol=satb2

Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=af21834c&gene_symbol_exact_match=1&gene_symbol=dcx

A comprehensive transcriptional map of primate brain development

https://nemoanalytics.org/p?l=NeocortexDevoNHPInVivo&g=DCX

Spatiotemporal transcriptome of the human brain

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=1c4d919a&gene_symbol=dcx

Transcriptional landscape of the prenatal human brain

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX

Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=45193eeb&gene_symbol_exact_match=1&gene_symbol=dcx

Integrated transcriptome and proteome analysis in human brain organoids reveals translational regulation of ribosomal proteins

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ed029ae1&gene_symbol_exact_match=1&gene_symbol=satb2

Distinct roles of Fto and Mettl3 in controlling development of the cerebral cortex through transcriptional and translational regulations

Cell Death and Disease, 2021

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=54ed44b9&gene_symbol_exact_match=1&gene_symbol=dcx

Developmental Dynamics of RNA Translation in the Human Brain

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9af49050&gene_symbol_exact_match=1&gene_symbol=dcx

Single-cell epigenomics reveals mechanisms of human cortical development

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=181e28bd&gene_symbol_exact_match=1&gene_symbol=dcx

Embryo-scale, single cell spatial transcriptomics

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=1527c089&gene_symbol_exact_match=1&gene_symbol=dcx

Molecular identity of human outer radial glia during cortical development

https://nemoanalytics.org/p?l=NeocortexDevoHsInVivo&g=FEZF2

Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX

The single-cell transcriptional landscape of mammalian organogenesis

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=83541e11&gene_symbol_exact_match=1&gene_symbol=dcx

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ad778833&gene_symbol_exact_match=1&gene_symbol=dcx

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=b8eb0718&gene_symbol_exact_match=1&gene_symbol=dcx

In vitro characterization of the human segmentation clock

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d1d15855&gene_symbol_exact_match=1&gene_symbol=dcx

Single-cell analysis of long non-coding RNAs in the developing human neocortex

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=da3e333e&gene_symbol_exact_match=1&gene_symbol=dcx

Primate gastrulation and early organogenesis at single-cell resolution

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9aa56652&gene_symbol_exact_match=1&gene_symbol=dcx

MYT1L deficiency impairs excitatory neuron trajectory during cortical development

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=cb8e7628&gene_symbol_exact_match=1&gene_symbol=dcx

Interneuron origin and molecular diversity in the human fetal brain

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=0f2b4a66&gene_symbol=hopx

Pluripotent stem cell-derived model of the post-implantation human embryo

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=6b3de8f5&gene_symbol_exact_match=1&gene_symbol=sox2

Early role for a Na+,K+-ATPase (ATP1A3) in brain development

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=361ec951&gene_symbol=dcx

Single-cell transcriptomic characterization of a gastrulating human embryo

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=441ad3f0&gene_symbol=dcx

Robust production of uniform human cerebral organoids from pluripotent stem cells

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=26e5fc11&gene_symbol_exact_match=1&gene_symbol=dcx

A human cell atlas of fetal gene expression

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=f940e386&gene_symbol=eomes

A single-cell transcriptome atlas profiles early organogenesis in human embryos

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=1e6b3886&gene_symbol=dcx

nemo includes head only for now (add these to ctx devo profiles!) - add more/all early cells: /dcs05/carlo/legacy-dcl01-ccolantu/data/Explr/SCrnaEarlyEmbryogenesis/FullData100k

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

https://nemoanalytics.org/p?l=NeocortexDevoHsInVitro&g=DCX

Progenitor cell diversity in the developing mouse neocortex

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=92b3522a&gene_symbol=dcx

An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics

https://nemoanalytics.org//index.html?layout_id=a835ce64&gene_symbol_exact_match=1

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

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=4e12a525&gene_symbol_exact_match=1&gene_symbol=dcn

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx

Primary, Organoid; Primary; Organoid

GW 4-40, DPO 4-15 weeks; GW4-15; 8-24 weeks

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx

Generating human neural diversity with a multiplexed morphogen screen in organoids

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=1252fd0b&gene_symbol_exact_match=1&gene_symbol=dcx

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx

Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon

Nenad Sestan, Pasko Rakic

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=c23b3f56&gene_symbol_exact_match=1&gene_symbol=RSPO3

Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=Jourdon2023&gene_symbol_exact_match=1&gene_symbol=dcx

Purification and characterization of human neural stem and progenitor cells

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=8f960f3b&gene_symbol_exact_match=1&gene_symbol=hopx

GW16-19; 12 Ab sorted cell types; SMARTseq2/3

Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration

https://nemoanalytics.org/index.html?multigene_plots=0&gene_symbol_exact_match=1&gene_symbol=dcx

Engineering of human brain organoids with a functional vascular-like system

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=8d2e7d9f&gene_symbol_exact_match=1&gene_symbol=stmn2

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX

Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=6019924a&gene_symbol_exact_match=1&gene_symbol=dcx

Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=0955d85f&gene_symbol_exact_match=1&gene_symbol=dcx

General anesthetic action profile on the human prefrontal cortex cells through comprehensive single-cell RNA-seq analysis

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=05bf6ee4&gene_symbol_exact_match=1&gene_symbol=satb2

Individual human cortical progenitors can produce excitatory and inhibitory neurons

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d2566643&gene_symbol_exact_match=1&gene_symbol=satb2

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx

A single cell transcriptomic atlas of human neocortical development during mid-gestation.

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Polioudakis2019&gene_symbol=DCX

Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development

https://nemoanalytics.org/p?l=NeocortexDevoHsInVivo&g=FEZF2

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

https://nemoanalytics.org/p?l=NeocortexDevoHsInVivo&g=FEZF2

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a7059ceb&gene_symbol=hopx

Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=6a3778b1&gene_symbol_exact_match=1&gene_symbol=dcx

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development

https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=9e1ec864&gene_symbol=dcx

Assembly of functionally integrated human forebrain spheroids

https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=Birey2017&gene_symbol_exact_match=1&gene_symbol=dcx

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

https://nemoanalytics.org/p?l=Velasco2019&g=DCX

Self-patterned WBO: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659341/; Dorsally Patterned Organoids: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864329/; Dorsal Patterned Spheroids: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912437/; Ventral Patterned Spheroids: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912437/

Cell Stress in Cortical Organoids Impairs Molecular Subtype Specification

In Vivo: https://nemoanalytics.org/p?l=Bhaduri2020.inVivo&g=EOMES; In Vitro - all: https://nemoanalytics.org/p?l=e61a94a2&g=EOMES; 1 line, Multiprotocol and Timecourse: https://nemoanalytics.org/p?l=eb1414cf&g=EOMES; Indiv Organoids: https://nemoanalytics.org/p?l=f0230123&g=EOMES; 1Prot1Line: https://nemoanalytics.org/p?l=b3439bc6&g=EOMES; 1 Prot: https://nemoanalytics.org/p?l=90b9499d&g=EOMES