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1
Journal, YearFirst AuthorLast AuthorData Type (s)
Data Source
Nemo ProfileSpeciesSystemTime periodBrain Region / Patterning
2
Molecular identity of human outer radial glia during cortical development
Cell, 2015Alex PollenArnold KreigsteinscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
HsPrimaryGW16-18
3
Single-cell analysis of long non-coding RNAs in the developing human neocortex
Genome Biol, 2016Siyuan John LiuArnold KreigsteinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX
HsPrimary
4
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex
Science, 2017NowakowskiArnold KriegsteinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx
HsPrimaryGW6-37
5
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Cell, 2019Alex PollenArnold KriegsteinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx
HsPrimary
Hs in vivo: GW 4-40; Macaque in vivo: GW4-15; Hs in vitro (DPO): 4-15 weeks; Chimp in vitro: 8-24 weeks
6
Cell Stress in Cortical Organoids Impairs Molecular Subtype Specification
Nature, 2020Aparna BhaduriArnold KriegsteinscRNAseqSource
Bhaduri2020CellStress - 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.
HsOrganoid
7
Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma
Cell SC, 2020Aparna BhaduriArnold KriegsteinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=8e051b15&gene_symbol=hopx
HsPrimary
8
Single-cell genomics identifies cell type–specific molecular changes in autism
Science, 2020Dmitry VelmeshevArnold KriegsteinsnRNAseqSourceHsPrimary
postnatal (4-22yrs) - 41 cortical samples from 2 cortical regions across 16 control and 15 ASD donors
9
An atlas of cortical arealization identifies dynamic molecular signatures
Nature, 2021Aparna BhaduriArnold KriegsteinscRNAseq, smFISHSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=3587049a&gene_symbol=dcx AND https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d14afd3b&gene_symbol_exact_match=1&gene_symbol=satb2
HsPrimaryGW 14-25FB, MB, HB
10
Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia
Nature Neuro, 2021Ugomma EzeArnold KriegsteinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a7059ceb&gene_symbol=hopx
HsPrimaryGW6-10
telencephalon, diencephalon, midbrain, hindbrain, cerebellum, ganglionic eminences, thalamus, hypothalamus and cortex
11
Single-cell analysis of prenatal and postnatal human cortical development
Science 2023Dmitry VelmeshevArnold KriegsteinsnRNAseqSourceHsPrimarypre and post-natal
12
A cross-species proteomic map reveals neoteny of human synapse development
Nature, 2023Li WangArnold Kriegsteinbulk proteomicsSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=5fdff881&gene_symbol_exact_match=1&gene_symbol=dcx
Hs, MacMul, Mm
PrimaryGW18, 22, 28, Yr 0.1, 4.0, 18.0
13
Individual human cortical progenitors can produce excitatory and inhibitory neurons
Nature, 2021Ryan DelgadoTomasz NowakowskiscRNAseqSourceHs
14
Single-cell epigenomics reveals mechanisms of human cortical development
Nature, 2021Ryan ZiffraTomasz Nowakowski
scATACseq (scRNAseq from arealization)
SourceHsPrimarymid gestation 15-20ish
15
The development and evolution of inhibitory neurons in primate cerebrum
Nature, 2022Matthew SchmitzAlex PollenscRNAseqSourceMm, MacMulPrimarydid not yet get mose data
16
Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes
Science, 2022Denise E. AllenTomasz NowakowskiPatch-seqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=45193eeb&gene_symbol_exact_match=1&gene_symbol=dcx
Hs
17
Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus
bioRxiv, 2022Matthew Heffel
Tomasz Nowakowski, Chongyuan Luo
sn-m3C-seqSource
18
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
PNAS, 2015J. Gray CampBarbara TreutleinscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx
HsOrganoid+PrimaryGW12-13
19
Organoid single-cell genomic atlas uncovers human-specific features of brain development
Nature, 2019Sabina Kanton
Barbara Treutlein, Arnold Kriegstein
scRNAseq, ATACseqSource
https://nemoanalytics.org/p?l=Kanton2019&g=DCX
Hs, MacMul, Chimp
Organoid+Primary
0d, 4d, 10d, 15d, 1m, 2m, 4m
20
Lineage recording in human cerebral organoidsNat. Methods, 2021Zhisong HeBarbara Treutlein
scRNAseq, Lineage Tracing, VISIUM
Source
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=96e50e10&gene_symbol=dcx
HsOrganoid1M, 1.5M, 2M
21
Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases
Cell SC, 2021Jonas FleckBarbara TreutleinISH, bulkRNAseq, scRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=3618a37f&gene_symbol=dcx
Hs, MmPrimary
we grabbed the VoxHunt data that is re-organized data derived from the allen brain inst. mouse developing brain ISH
22
Inferring and perturbing cell fate regulomes in human cerebral organoids
Nature, 2022Jonas FleckBarbara Treutlein
Raw sequencing data are available at ArrayExpress. The accessions for the individual experiments are E-MTAB-12001 for developmental time course scRNA-seq data, E-MTAB-11998 for developmental time course scATAC-seq data, E-MTAB-12004 for multiome data of the neuroepithelial stage, E-MTAB-11999 for scRNA-seq data of the CROP-seq experiment, E-MTAB-12005 for amplicon sequencing of the CROP-seq experiment, E-MTAB-11997 for scRNA-seq data of GLI3-KO organoids, E-MTAB-12002 for multiome data of GLI3-KO organoids, E-MTAB-12003 for multiome data of SHH-treated organoids and E-MTAB-12006 for CUT&Tag data. Processed data and the VCF files for demultiplexing are available at Zenodo (https://doi.org/10.5281/zenodo.5242913).
SourceHsOrganoid
Data availability: Raw sequencing data are available at ArrayExpress. The accessions for the individual experiments are E-MTAB-12001 for developmental time course scRNA-seq data, E-MTAB-11998 for developmental time course scATAC-seq data, E-MTAB-12004 for multiome data of the neuroepithelial stage, E-MTAB-11999 for scRNA-seq data of the CROP-seq experiment, E-MTAB-12005 for amplicon sequencing of the CROP-seq experiment, E-MTAB-11997 for scRNA-seq data of GLI3-KO organoids, E-MTAB-12002 for multiome data of GLI3-KO organoids, E-MTAB-12003 for multiome data of SHH-treated organoids and E-MTAB-12006 for CUT&Tag data. Processed data and the VCF files for demultiplexing are available at Zenodo (https://doi.org/10.5281/zenodo.5242913).
23
Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells
Neuron, 2017Steven A. SloanSergiu Pasca
bulkRNAseq, scRNAseq (d100-d450)
Source (sc)
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=408a33fc&gene_symbol=dcx
HsOrganoid+Primary3M, 15M
24
Assembly of functionally integrated human forebrain spheroids
Nature, 2017Fikri BireySergiu PascascRNAseq
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93811; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96045
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=1f68bd16&gene_symbol=dcx
HsOrganoid3M, 4M (lineage tracing)Pallium (hCS), Subpallium (hSS)
25
Reliability of human 3D cortical organoid generation
Nat Methods, 2019Se-Jin YoonSergiu Pasca
scRNAseq (d105), bulk RNAseq (d25-d100)
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107771; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120700
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=7e146d6e&gene_symbol=dcx
HsOrganoid1M, 2M, 3M
26
Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures
Nat Neuro, 2019Rebecca MartonSergiu PascascRNAseqSourceHsOrganoidd127 (this study)hOLS
27
Generation of Functional Human 3D Cortico-Motor Assembloids
Cell, 2020Jimena AndersenSergiu PascascRNAseqSourceHs
28
Long Term Maturation of Human Cortical Organoids Matches Key Early Postnatal Transitions
Nat Neuro, 2021Aaron Gordon
Sergiu Pasca, Daniel Geschwind
bulkRNAseq, DNA methylationSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=acff3407&gene_symbol=dcx
Hs
29
Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
Cell, 2021Alexandro Trevino
Sergiu Pasca, William Greenleaf
scRNAseq, scATACseq???
https://nemoanalytics.org/p?l=Trevino2021&g=EOMES
HsPrimaryGW16,20,21,24
30
Dissecting the molecular basis of human interneuron migration in forebrain assembloids from Timothy syndrome
Cell Stem Cell, 2022Fikri BireySergiu PascaSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=bae433b5&gene_symbol=olig1
HsOrganoidd40-129hCS, hSS
31
Generating human neural diversity with a multiplexed morphogen screen in organoids
BiorXiv, 2023Neal AminSergiu PascascRNAseqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=1252fd0b&gene_symbol_exact_match=1&gene_symbol=dcx
HsOrganoidd70
32
A single cell transcriptomic atlas of human neocortical development during mid-gestation.
Neuron, 2019Damon PolioudakisDaniel GeschwindscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Polioudakis2019&gene_symbol=DCX
HsPrimaryGW16
33
Cell diversity and network dynamics in photosensitive human brain organoids
Nature, 2017Giorgia QuadratoPaola ArlottascRNAseqSource
looks like this was prepped for nemo upload, but is not there - is this correct?
HsOrganoid3M, 6MSelf-patterned WBO
34
Individual brain organoids reproducibly form cell diversity of the human cerebral cortex
Nature, 2019Silvia VelascoPaola ArlottascRNAseqSource
https://nemoanalytics.org/p?l=Velasco2019&g=DCX
HsOrganoid3M, 6M
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/
35
Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex
Nature, 2021Daniela Di BellaPaola Arlotta
scRNAseq, scATACseq, Slide-seq v2 - where is this spatial data - no reference in paper
Source
https://nemoanalytics.org/p?l=DiBella2021&g=eomes
MmPrimaryE10.5 - P4Somatosensory Cortex
36
Autism genes converge on asynchronous development of shared neuron classes
Nature, 2022Bruna PaulsenPaola ArlottascRNAseq, scATACseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Paulsen2022&gene_symbol=hopx
HsOrganoid1M, 3M, 6MDorsally Patterned Organoid
37
Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex
Cell, 2022Ana UzquianoPaola Arlotta
scRNAseq, SLIDE-seq, ATACseq
Source
https://nemoanalytics.org/p?&l=Uzquiano2022&g=dcx
HsOrganoid
23day, 1mo, 1.5mo, 2mo, 3mo, 4mo, 5mo, 6mo
Dorsally Patterned Organoid
38
Spatiotemporal transcriptome of the human brainNature, 2011Hyo Jung KangNenad Sestanbulk microarraysSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=1c4d919a&gene_symbol=dcx
Hs
39
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia
Cell Rep, 2016Marco OnoratiNenad SestanscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX
Hs
40
Spatiotemporal transcriptomic divergence across human and macaque brain development
Science, 2018Ying ZhuNenad SestanbulkRNAseq, scRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=d416d7e8&gene_symbol=dcx
Hs, MacMul, PanTrog?
PrimaryFetal, Adult
looks like we only have macaqe for this - where is chimp? is human just brainspan or is this and/or souza human data different?
41
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Science, 2018Mingfeng LiNenad Sestan
bulkRNAseq, scRNAseq, H3K27ac
Source
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=72656283&gene_symbol=dcx
HsPrimaryFetal, Adult7 neocortical regions, 4 others
42
Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon
Science 2023Nicola MicaliPasko RakicscRNAseq
The scRNA-seq data were deposited in the NEMO Archive (RRID:SCR_002001) under identifier dat-fjx1jbr accessible at https://assets.nemoarchive.org/dat-fjx1jbr. The data can also be interactively visualized at http://resources.sestanlab.org/devmacaquebrain.
https://nemoanalytics.org/p?l=CtxDevo3mamm&g=EOMES
MacMulPrimary
E37-110 (83 samples, 761,529 cells)
43
Transcriptomic Taxonomy and Neurogenic Trajectories of Adult Human, Macaque and Pig Hippocampal and Entorhinal Cells
Neuron, 2023Daniel FranjicNenad SestansnRNAseq
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx
Hs, MacMul, Pig
PrimaryAdult
44
Early role for a Na+,K+-ATPase (ATP1A3) in brain development
PNAS, 2021Richard SmithChris WalshscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=361ec951&gene_symbol=dcx
HsPrimaryfetal and infant
45
Integrated transcriptome and proteome analysis in human brain organoids reveals translational regulation of ribosomal proteins
Elife, 2023Jaydeep SidhayeJurgen KnoblichRNAseq, ProteomicsSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ed029ae1&gene_symbol_exact_match=1&gene_symbol=satb2
HsOrganoidsd20-120, d37 (ribo)
46
Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain
Cell Rep, 2020Yoshiaki TanakaIn-Hyun ParkscRNAseqSourceHsOrganoid
47
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis
Cell Res, 2018Xiaoying FanFuchou TangscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
HsPrimaryGW22-23
48
Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development
Sci Adv, 2020Xiaoying FanFuchou TangscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
HsPrimaryGW7-28
49
Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development
Dev Cell, 2018Sueli MarquesGonçalo Castelo-BrancoscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=9e1ec864&gene_symbol=dcx
MmPrimaryBrain, Spinal Cord
50
Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis
Dev Cell, 2022David van BruggenGonçalo Castelo-BrancoscRNAseq, scATACseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=9e1ec864&gene_symbol=dcx
HsPrimary
51
Cortical organoids model early brain development disrupted by 16p11.2 CNV in autism
Mol Psych, 2021Jorge UrrestiAlysson Muotri
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=300f7fec&gene_symbol=hopx
Hs
52
A human cell atlas of fetal gene expressionScience, 2021Junyue CaoJay ShendurescRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=f940e386&gene_symbol=eomes
HsPrimaryGW16-17
53
A comprehensive transcriptional map of primate brain development
Nature, 2016Tyrgve BakkenEd LeinMicroarray
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
MacMul
54
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Nature, 2021Tyrgve BakkenEd LeinSmart-seqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ac9863bf&gene_symbol_exact_match=1&gene_symbol=dcx
Hs, Mm, Marmoset
adult
55
Transcriptional landscape of the prenatal human brain
Nature, 2014Jeremy MillerEd LeinMicroarray
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
Hs
56
Evolutionary Changes in Promoter and Enhancer Activity During Human Corticogenesis
Science, 2015Steven ReillyPasko Rakic, James NoonanCHIPseqSource
Hs, MacMul, Mm
PrimaryHuman: GW7, 8.5, 12
Whole Cortex (GW7, 8.5). Frontal and Occipital (GW12)
57
Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids
Nat Comm, 2023Rebecca SebastianChangHui PakscRNAseqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=6a3778b1&gene_symbol_exact_match=1&gene_symbol=dcx
HsOrganoid
58
Induction of myelinating oligodendrocytes in human cortical spheroids
Nat. Met., 2018Mayur MadhavanPaul J. TesarbulkRNAseq, scRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=74b652f6&gene_symbol=dcx
HshCS and hOCSd92Dorsal Forebrain + Oligo Growth Factors
59
A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development
Cell SC, 2017Zizhen YaoSharad RamanathanscRNAseq
https://nemoanalytics.org/p?l=NeocortexDevoHsInVitro&g=DCX
Hs2D
60
Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates
Cell Rep, 2020Nicola MicaliRonald McKaybulkRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=NeocortexEvoDevo&gene_symbol=DCX
Mm - bulkRNA-seq - primary NSC from E11 in vitro with differing FGF2 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144158; Hs - bulkRNA-seq - passaging of iPSC-derived NSCs - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144156; Hs - bulkRNA-seq - differentiation of iPSC-derived NSCs - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144157; MacMul - scRNAseq V1 E77/78 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144508
61
CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells
Neuron, 2014Joyce van de LeemputChristopher FasanobulkRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX
Hsin virto
62
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
Nat Neuro, 2018Andrew JaffeDaniel WeinbergerbulkRNAseq
https://nemoanalytics.org/p?l=NeocortexEvoDevo&g=FEZF2
Hs 2D
63
Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Nat Comm, 2020Emily BurkeAndrew Jaffebulk RNAseq
https://nemoanalytics.org/p?l=2cfae2bd&g=DCX
Hs 2D
64
Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes
Stem Cell Rep, 2019Andrew FieldsDavid HausslerbulkRNAseq, scRNAseq(sc) Source,
https://nemoanalytics.org/p?l=NeocortexDevoNHPInVitro&g=DCX
65
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
ELife, 2016
Felipe Mora-Bermudez
Weiland HuttnerscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx
Hs, ChimpOrganoid
66
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Nature, 2023Di ZhangRong Fan
Spatial ATAC-RNA, Spatial Cut&Tag
Source
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=5de0f884&gene_symbol_exact_match=1&gene_symbol=hopx
Mm, HsPrimary
67
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
Cell, 2022Ao ChenJian WangStereo-seq, spatial nanoballsSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=286120a6&gene_symbol_exact_match=1&gene_symbol=dcx
MmPrimaryE9.5-16.5, AdultFull embryo, Brain
68
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Nat Neuro, 2021Kristen MaynardAndrew JaffeVISIUMSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=c9f4dd06&gene_symbol_exact_match=1&gene_symbol=pcp4
HsPrimaryAdult
69
Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex
Science, 2019Ludovic TelleyDenis JabaudonSmart-seq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Telley2019&gene_symbol=DCX
MmPrimary
70
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex
Nature, 2018Suijuan ZhongXiaoqun WangscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
HsPrimaryGW8-26
71
Molecular architecture of the developing mouse brain
Nature, 2021Gioele La MannoSten Linnarsson
scRNAseq, in situ RNA sequencing
https://nemoanalytics.org/p?l=LaManno2021.byAge&g=DCX and https://nemoanalytics.org/p?l=LaManno2021.byTissue
MmPrimaryE7-18
72
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal
PNAS, 2012Simone FietzWieland HuttnerbulkRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX
Hs, MmPrimaryGW13-16
73
A survey of human brain transcriptome diversity at the single cell level
PNAS, 2015Spyros DarmanisStephen QuakescRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX
HsPrimary
74
Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse
Neuron, 2016Ye ZhangBen BarresbulkRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a613d976&gene_symbol=dcx
Hs, MmPrimaryGW17-20Temporal Lobe
75
Progenitor cell diversity in the developing mouse neocortex
PNAS, 2021Xiangbin RuanXiaochang ZhangscRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=92b3522a&gene_symbol=dcx
MmPrimary
76
Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy
Nat Commun, 2020Charles CoutourierKevin PetreccascRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=80721e4f&gene_symbol=dcx
HsPrimary
GW13, 17, 19, 21, 23: 23k cells
77
Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation
Cell, 2018Ikuo SuzukiPierre VanderhagenbulkRNAseq
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a445a5fc&gene_symbol=dcx
HsPrimary
78
Interneuron origin and molecular diversity in the human fetal brain
Nat Neuro, 2021Yuan YuTao SunscRNAseqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=0f2b4a66&gene_symbol=hopx
HsPrimary
79
Shared and distinct transcriptomic cell types across neocortical areas
Nature, 2018Bosiljka TasicHongkui ZhengSmart-seqSource
https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a0f9fedd&gene_symbol=dcx
MmPrimaryAdult ALM, V1
80
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
Nat Neurosci 2016Bosiljka TasicHongkui ZengsnRNAseqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=3c1898ac&gene_symbol_exact_match=1&gene_symbol=dcx
MmPrimaryAdult (8 week)V1, layer dissections
81
Multi-omic profiling of the developing human cerebral cortex at the single cell level
Sci Adv, 2023Kaiyi ZhuPanos RoussosscRNAseq, scATACseqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=79e1825f&gene_symbol_exact_match=1&gene_symbol=eomes
HsPrimaryFetal and Lifespan
82
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
Cell, 2022Charles HerringRyan ListersnRNAseq, snATACseqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9fe511b4&gene_symbol_exact_match=1&gene_symbol=dcx
HsPrimaryFetal and Lifespan
83
Single-Nuclei RNA Sequencing of 5 Regions of the Human Prenatal Brain Implicates Developing Neuron Populations in Genetic Risk for Schizophrenia
Biological Psychiatry, 2022
Darren CameronNicholas BraysnRNAseqSource
https://nemoanalytics.org/p?l=d5992ff7&g=FEZF2
HsPrimaryFC, GE, Hip, Thal, Cerebellum
84
An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics
Nat Comm, 2022Susana RamosNadejda TsankovascRNAseq
https://nemoanalytics.org//index.html?layout_id=a835ce64&gene_symbol_exact_match=1
HsPrimaryGW 17-41Germinal Zone and CP
85
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Science 2023Nikolas JorstadEd LeinSmart-seqSourceHsPrimaryAdult
50k cells, 8 neocortical regions, layer dissection
86
Spatiotemporal proteomic atlas of multiple brain regions across early fetal to neonatal stages in cynomolgus monkey
Nat Comm, 2023Jingkuan WeiWei SiProteomicsSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=f2ffb73b&gene_symbol_exact_match=1&gene_symbol=hopx
Cyn MonkeyprimaryFetal and 1 postnatalMany regions
87
Developmental Dynamics of RNA Translation in the Human Brain
Nat Neuro, 2022Erin DuffyMichael GreenbergRNAseq, RiboSeqSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9af49050&gene_symbol_exact_match=1&gene_symbol=dcx
HsPrimary
88
Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex
Nat Comm, 2023Iva Salamon Mladen-Roko Rasin
snRNAseq, Polysome Profiling, RIP-seq
Source
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=babd289d&gene_symbol_exact_match=1&gene_symbol=dcx
Hs, MmPrimaryGW11-GW20
89
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
Nature, 2021Meng ZhangXiaowei ZhuangMERFISHSource
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=7e14ad94&gene_symbol_exact_match=1&gene_symbol=satb2
MmPrimaryAdultMOp
90
Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer's disease
Genome Med, 2016Minghui WangBin ZhangMicroarray
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=db52d017&gene_symbol_exact_match=1&gene_symbol=satb2
HsPrimaryAdult
91
Dissecting neural differentiation regulatory networks through epigenetic footprinting
Nature, 2015Michael ZillerAlexander MeissnerRNAseq
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2cfae2bd&gene_symbol_exact_match=1&gene_symbol=dcx
Hs2D
92
Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors
Nat Commun, 2015Reuven EdriYechiel ElkabetzMicroarray
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2cfae2bd&gene_symbol_exact_match=1&gene_symbol=dcx
Hs2D
93
Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing
Nat Neuro, 2018Hannah HochgernerSten LinnarssonscRNAseq
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx
MmPrimaryAdult
94
Decoding the development of the human hippocampus
Nature 2020Suijuan ZhongXiaoqun WangscRNA-seq, scATACseq
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx
HsPrimaryfetal: GW16–27
95
Spatiotemporal molecular dynamics of the developing human thalamus
Science, 2023Chang KimTomasz NowakowskiscRNAseq, MERFISH
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=b0019b85&gene_symbol_exact_match=1&gene_symbol=dcx
HsPrimary
96
Conserved cell types with divergent features in human versus mouse cortex
Nature, 2019Rebecca HodgeEd LeinsmartSeq
https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=0e5c2656&gene_symbol_exact_match=1&gene_symbol=dcx
Hs, MmPrimaryMTG, layer dissections
97
Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain
Nat Neuro, 2023Aritra BhatacharjeeYi ZhangMERFISHSourceMmprimaryAdultPFC
98
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