A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | |
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1 | Journal, Year | First Author | Last Author | Data Type (s) | Data Source | Nemo Profile | Species | System | Time period | Brain Region / Patterning | ||||||||||||||||
2 | Molecular identity of human outer radial glia during cortical development | Cell, 2015 | Alex Pollen | Arnold Kreigstein | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX | Hs | Primary | GW16-18 | |||||||||||||||||
3 | Single-cell analysis of long non-coding RNAs in the developing human neocortex | Genome Biol, 2016 | Siyuan John Liu | Arnold Kreigstein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX | Hs | Primary | |||||||||||||||||
4 | Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex | Science, 2017 | Nowakowski | Arnold Kriegstein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx | Hs | Primary | GW6-37 | ||||||||||||||||
5 | Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution | Cell, 2019 | Alex Pollen | Arnold Kriegstein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx | Hs | Primary | 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, 2020 | Aparna Bhaduri | Arnold Kriegstein | scRNAseq | Source | 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. | Hs | Organoid | |||||||||||||||||
7 | Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma | Cell SC, 2020 | Aparna Bhaduri | Arnold Kriegstein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=8e051b15&gene_symbol=hopx | Hs | Primary | |||||||||||||||||
8 | Single-cell genomics identifies cell type–specific molecular changes in autism | Science, 2020 | Dmitry Velmeshev | Arnold Kriegstein | snRNAseq | Source | Hs | Primary | 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, 2021 | Aparna Bhaduri | Arnold Kriegstein | scRNAseq, smFISH | Source | 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 | Hs | Primary | GW 14-25 | FB, MB, HB | |||||||||||||||
10 | Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia | Nature Neuro, 2021 | Ugomma Eze | Arnold Kriegstein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a7059ceb&gene_symbol=hopx | Hs | Primary | GW6-10 | telencephalon, diencephalon, midbrain, hindbrain, cerebellum, ganglionic eminences, thalamus, hypothalamus and cortex | |||||||||||||||
11 | Single-cell analysis of prenatal and postnatal human cortical development | Science 2023 | Dmitry Velmeshev | Arnold Kriegstein | snRNAseq | Source | Hs | Primary | pre and post-natal | |||||||||||||||||
12 | A cross-species proteomic map reveals neoteny of human synapse development | Nature, 2023 | Li Wang | Arnold Kriegstein | bulk proteomics | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=5fdff881&gene_symbol_exact_match=1&gene_symbol=dcx | Hs, MacMul, Mm | Primary | GW18, 22, 28, Yr 0.1, 4.0, 18.0 | ||||||||||||||||
13 | Individual human cortical progenitors can produce excitatory and inhibitory neurons | Nature, 2021 | Ryan Delgado | Tomasz Nowakowski | scRNAseq | Source | Hs | |||||||||||||||||||
14 | Single-cell epigenomics reveals mechanisms of human cortical development | Nature, 2021 | Ryan Ziffra | Tomasz Nowakowski | scATACseq (scRNAseq from arealization) | Source | Hs | Primary | mid gestation 15-20ish | |||||||||||||||||
15 | The development and evolution of inhibitory neurons in primate cerebrum | Nature, 2022 | Matthew Schmitz | Alex Pollen | scRNAseq | Source | Mm, MacMul | Primary | did not yet get mose data | |||||||||||||||||
16 | Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes | Science, 2022 | Denise E. Allen | Tomasz Nowakowski | Patch-seq | Source | 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, 2022 | Matthew Heffel | Tomasz Nowakowski, Chongyuan Luo | sn-m3C-seq | Source | ||||||||||||||||||||
18 | Human cerebral organoids recapitulate gene expression programs of fetal neocortex development | PNAS, 2015 | J. Gray Camp | Barbara Treutlein | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx | Hs | Organoid+Primary | GW12-13 | ||||||||||||||||
19 | Organoid single-cell genomic atlas uncovers human-specific features of brain development | Nature, 2019 | Sabina Kanton | Barbara Treutlein, Arnold Kriegstein | scRNAseq, ATACseq | Source | 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 organoids | Nat. Methods, 2021 | Zhisong He | Barbara 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 | Hs | Organoid | 1M, 1.5M, 2M | ||||||||||||||||
21 | Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases | Cell SC, 2021 | Jonas Fleck | Barbara Treutlein | ISH, bulkRNAseq, scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=3618a37f&gene_symbol=dcx | Hs, Mm | Primary | 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, 2022 | Jonas Fleck | Barbara 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). | Source | Hs | Organoid | 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, 2017 | Steven A. Sloan | Sergiu 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 | Hs | Organoid+Primary | 3M, 15M | ||||||||||||||||
24 | Assembly of functionally integrated human forebrain spheroids | Nature, 2017 | Fikri Birey | Sergiu Pasca | scRNAseq | 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 | Hs | Organoid | 3M, 4M (lineage tracing) | Pallium (hCS), Subpallium (hSS) | |||||||||||||||
25 | Reliability of human 3D cortical organoid generation | Nat Methods, 2019 | Se-Jin Yoon | Sergiu 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 | Hs | Organoid | 1M, 2M, 3M | ||||||||||||||||
26 | Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures | Nat Neuro, 2019 | Rebecca Marton | Sergiu Pasca | scRNAseq | Source | Hs | Organoid | d127 (this study) | hOLS | ||||||||||||||||
27 | Generation of Functional Human 3D Cortico-Motor Assembloids | Cell, 2020 | Jimena Andersen | Sergiu Pasca | scRNAseq | Source | Hs | |||||||||||||||||||
28 | Long Term Maturation of Human Cortical Organoids Matches Key Early Postnatal Transitions | Nat Neuro, 2021 | Aaron Gordon | Sergiu Pasca, Daniel Geschwind | bulkRNAseq, DNA methylation | Source | 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, 2021 | Alexandro Trevino | Sergiu Pasca, William Greenleaf | scRNAseq, scATACseq | ??? | https://nemoanalytics.org/p?l=Trevino2021&g=EOMES | Hs | Primary | GW16,20,21,24 | ||||||||||||||||
30 | Dissecting the molecular basis of human interneuron migration in forebrain assembloids from Timothy syndrome | Cell Stem Cell, 2022 | Fikri Birey | Sergiu Pasca | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=bae433b5&gene_symbol=olig1 | Hs | Organoid | d40-129 | hCS, hSS | ||||||||||||||||
31 | Generating human neural diversity with a multiplexed morphogen screen in organoids | BiorXiv, 2023 | Neal Amin | Sergiu Pasca | scRNAseq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=1252fd0b&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Organoid | d70 | ||||||||||||||||
32 | A single cell transcriptomic atlas of human neocortical development during mid-gestation. | Neuron, 2019 | Damon Polioudakis | Daniel Geschwind | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Polioudakis2019&gene_symbol=DCX | Hs | Primary | GW16 | ||||||||||||||||
33 | Cell diversity and network dynamics in photosensitive human brain organoids | Nature, 2017 | Giorgia Quadrato | Paola Arlotta | scRNAseq | Source | looks like this was prepped for nemo upload, but is not there - is this correct? | Hs | Organoid | 3M, 6M | Self-patterned WBO | |||||||||||||||
34 | Individual brain organoids reproducibly form cell diversity of the human cerebral cortex | Nature, 2019 | Silvia Velasco | Paola Arlotta | scRNAseq | Source | https://nemoanalytics.org/p?l=Velasco2019&g=DCX | Hs | Organoid | 3M, 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, 2021 | Daniela Di Bella | Paola Arlotta | scRNAseq, scATACseq, Slide-seq v2 - where is this spatial data - no reference in paper | Source | https://nemoanalytics.org/p?l=DiBella2021&g=eomes | Mm | Primary | E10.5 - P4 | Somatosensory Cortex | |||||||||||||||
36 | Autism genes converge on asynchronous development of shared neuron classes | Nature, 2022 | Bruna Paulsen | Paola Arlotta | scRNAseq, scATACseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Paulsen2022&gene_symbol=hopx | Hs | Organoid | 1M, 3M, 6M | Dorsally Patterned Organoid | |||||||||||||||
37 | Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex | Cell, 2022 | Ana Uzquiano | Paola Arlotta | scRNAseq, SLIDE-seq, ATACseq | Source | https://nemoanalytics.org/p?&l=Uzquiano2022&g=dcx | Hs | Organoid | 23day, 1mo, 1.5mo, 2mo, 3mo, 4mo, 5mo, 6mo | Dorsally Patterned Organoid | |||||||||||||||
38 | Spatiotemporal transcriptome of the human brain | Nature, 2011 | Hyo Jung Kang | Nenad Sestan | bulk microarrays | Source | 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, 2016 | Marco Onorati | Nenad Sestan | scRNAseq | 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, 2018 | Ying Zhu | Nenad Sestan | bulkRNAseq, scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=d416d7e8&gene_symbol=dcx | Hs, MacMul, PanTrog? | Primary | Fetal, 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, 2018 | Mingfeng Li | Nenad Sestan | bulkRNAseq, scRNAseq, H3K27ac | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=72656283&gene_symbol=dcx | Hs | Primary | Fetal, Adult | 7 neocortical regions, 4 others | |||||||||||||||
42 | Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon | Science 2023 | Nicola Micali | Pasko Rakic | scRNAseq | 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 | MacMul | Primary | E37-110 (83 samples, 761,529 cells) | ||||||||||||||||
43 | Transcriptomic Taxonomy and Neurogenic Trajectories of Adult Human, Macaque and Pig Hippocampal and Entorhinal Cells | Neuron, 2023 | Daniel Franjic | Nenad Sestan | snRNAseq | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx | Hs, MacMul, Pig | Primary | Adult | |||||||||||||||||
44 | Early role for a Na+,K+-ATPase (ATP1A3) in brain development | PNAS, 2021 | Richard Smith | Chris Walsh | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=361ec951&gene_symbol=dcx | Hs | Primary | fetal and infant | ||||||||||||||||
45 | Integrated transcriptome and proteome analysis in human brain organoids reveals translational regulation of ribosomal proteins | Elife, 2023 | Jaydeep Sidhaye | Jurgen Knoblich | RNAseq, Proteomics | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=ed029ae1&gene_symbol_exact_match=1&gene_symbol=satb2 | Hs | Organoids | d20-120, d37 (ribo) | ||||||||||||||||
46 | Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain | Cell Rep, 2020 | Yoshiaki Tanaka | In-Hyun Park | scRNAseq | Source | Hs | Organoid | ||||||||||||||||||
47 | Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis | Cell Res, 2018 | Xiaoying Fan | Fuchou Tang | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX | Hs | Primary | GW22-23 | |||||||||||||||||
48 | Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development | Sci Adv, 2020 | Xiaoying Fan | Fuchou Tang | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX | Hs | Primary | GW7-28 | |||||||||||||||||
49 | Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development | Dev Cell, 2018 | Sueli Marques | Gonçalo Castelo-Branco | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=9e1ec864&gene_symbol=dcx | Mm | Primary | Brain, Spinal Cord | ||||||||||||||||
50 | Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis | Dev Cell, 2022 | David van Bruggen | Gonçalo Castelo-Branco | scRNAseq, scATACseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=9e1ec864&gene_symbol=dcx | Hs | Primary | |||||||||||||||||
51 | Cortical organoids model early brain development disrupted by 16p11.2 CNV in autism | Mol Psych, 2021 | Jorge Urresti | Alysson 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 expression | Science, 2021 | Junyue Cao | Jay Shendure | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=f940e386&gene_symbol=eomes | Hs | Primary | GW16-17 | ||||||||||||||||
53 | A comprehensive transcriptional map of primate brain development | Nature, 2016 | Tyrgve Bakken | Ed Lein | Microarray | 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, 2021 | Tyrgve Bakken | Ed Lein | Smart-seq | Source | 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, 2014 | Jeremy Miller | Ed Lein | Microarray | 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, 2015 | Steven Reilly | Pasko Rakic, James Noonan | CHIPseq | Source | Hs, MacMul, Mm | Primary | Human: 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, 2023 | Rebecca Sebastian | ChangHui Pak | scRNAseq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=6a3778b1&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Organoid | |||||||||||||||||
58 | Induction of myelinating oligodendrocytes in human cortical spheroids | Nat. Met., 2018 | Mayur Madhavan | Paul J. Tesar | bulkRNAseq, scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=74b652f6&gene_symbol=dcx | Hs | hCS and hOCS | d92 | Dorsal Forebrain + Oligo Growth Factors | |||||||||||||||
59 | A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development | Cell SC, 2017 | Zizhen Yao | Sharad Ramanathan | scRNAseq | https://nemoanalytics.org/p?l=NeocortexDevoHsInVitro&g=DCX | Hs | 2D | ||||||||||||||||||
60 | Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates | Cell Rep, 2020 | Nicola Micali | Ronald McKay | bulkRNAseq | 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, 2014 | Joyce van de Leemput | Christopher Fasano | bulkRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX | Hs | in virto | |||||||||||||||||
62 | Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis | Nat Neuro, 2018 | Andrew Jaffe | Daniel Weinberger | bulkRNAseq | https://nemoanalytics.org/p?l=NeocortexEvoDevo&g=FEZF2 | Hs | 2D | ||||||||||||||||||
63 | Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs | Nat Comm, 2020 | Emily Burke | Andrew Jaffe | bulk 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, 2019 | Andrew Fields | David Haussler | bulkRNAseq, 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 Huttner | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=77c897cc&gene_symbol=dcx | Hs, Chimp | Organoid | ||||||||||||||||||
66 | Spatial epigenome–transcriptome co-profiling of mammalian tissues | Nature, 2023 | Di Zhang | Rong 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, Hs | Primary | |||||||||||||||||
67 | Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays | Cell, 2022 | Ao Chen | Jian Wang | Stereo-seq, spatial nanoballs | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=286120a6&gene_symbol_exact_match=1&gene_symbol=dcx | Mm | Primary | E9.5-16.5, Adult | Full embryo, Brain | |||||||||||||||
68 | Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex | Nat Neuro, 2021 | Kristen Maynard | Andrew Jaffe | VISIUM | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=c9f4dd06&gene_symbol_exact_match=1&gene_symbol=pcp4 | Hs | Primary | Adult | ||||||||||||||||
69 | Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex | Science, 2019 | Ludovic Telley | Denis Jabaudon | Smart-seq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=Telley2019&gene_symbol=DCX | Mm | Primary | ||||||||||||||||||
70 | A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex | Nature, 2018 | Suijuan Zhong | Xiaoqun Wang | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX | Hs | Primary | GW8-26 | |||||||||||||||||
71 | Molecular architecture of the developing mouse brain | Nature, 2021 | Gioele La Manno | Sten Linnarsson | scRNAseq, in situ RNA sequencing | https://nemoanalytics.org/p?l=LaManno2021.byAge&g=DCX and https://nemoanalytics.org/p?l=LaManno2021.byTissue | Mm | Primary | E7-18 | |||||||||||||||||
72 | Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal | PNAS, 2012 | Simone Fietz | Wieland Huttner | bulkRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=2cfae2bd&gene_symbol=DCX | Hs, Mm | Primary | GW13-16 | |||||||||||||||||
73 | A survey of human brain transcriptome diversity at the single cell level | PNAS, 2015 | Spyros Darmanis | Stephen Quake | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=ChenEtAl2021&gene_symbol=DCX | Hs | Primary | ||||||||||||||||||
74 | Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse | Neuron, 2016 | Ye Zhang | Ben Barres | bulkRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a613d976&gene_symbol=dcx | Hs, Mm | Primary | GW17-20 | Temporal Lobe | |||||||||||||||
75 | Progenitor cell diversity in the developing mouse neocortex | PNAS, 2021 | Xiangbin Ruan | Xiaochang Zhang | scRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=92b3522a&gene_symbol=dcx | Mm | Primary | ||||||||||||||||||
76 | Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy | Nat Commun, 2020 | Charles Coutourier | Kevin Petrecca | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=80721e4f&gene_symbol=dcx | Hs | Primary | GW13, 17, 19, 21, 23: 23k cells | ||||||||||||||||
77 | Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation | Cell, 2018 | Ikuo Suzuki | Pierre Vanderhagen | bulkRNAseq | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a445a5fc&gene_symbol=dcx | Hs | Primary | ||||||||||||||||||
78 | Interneuron origin and molecular diversity in the human fetal brain | Nat Neuro, 2021 | Yuan Yu | Tao Sun | scRNAseq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=0f2b4a66&gene_symbol=hopx | Hs | Primary | |||||||||||||||||
79 | Shared and distinct transcriptomic cell types across neocortical areas | Nature, 2018 | Bosiljka Tasic | Hongkui Zheng | Smart-seq | Source | https://nemoanalytics.org/index.html?&gene_symbol_exact_match=1&multigene_plots=0&layout_id=a0f9fedd&gene_symbol=dcx | Mm | Primary | Adult | ALM, V1 | |||||||||||||||
80 | Adult mouse cortical cell taxonomy revealed by single cell transcriptomics | Nat Neurosci 2016 | Bosiljka Tasic | Hongkui Zeng | snRNAseq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=3c1898ac&gene_symbol_exact_match=1&gene_symbol=dcx | Mm | Primary | Adult (8 week) | V1, layer dissections | |||||||||||||||
81 | Multi-omic profiling of the developing human cerebral cortex at the single cell level | Sci Adv, 2023 | Kaiyi Zhu | Panos Roussos | scRNAseq, scATACseq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=79e1825f&gene_symbol_exact_match=1&gene_symbol=eomes | Hs | Primary | Fetal and Lifespan | ||||||||||||||||
82 | Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution | Cell, 2022 | Charles Herring | Ryan Lister | snRNAseq, snATACseq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9fe511b4&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Primary | Fetal 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 Cameron | Nicholas Bray | snRNAseq | Source | https://nemoanalytics.org/p?l=d5992ff7&g=FEZF2 | Hs | Primary | FC, GE, Hip, Thal, Cerebellum | ||||||||||||||||
84 | An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics | Nat Comm, 2022 | Susana Ramos | Nadejda Tsankova | scRNAseq | https://nemoanalytics.org//index.html?layout_id=a835ce64&gene_symbol_exact_match=1 | Hs | Primary | GW 17-41 | Germinal Zone and CP | ||||||||||||||||
85 | Transcriptomic cytoarchitecture reveals principles of human neocortex organization | Science 2023 | Nikolas Jorstad | Ed Lein | Smart-seq | Source | Hs | Primary | Adult | 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, 2023 | Jingkuan Wei | Wei Si | Proteomics | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=f2ffb73b&gene_symbol_exact_match=1&gene_symbol=hopx | Cyn Monkey | primary | Fetal and 1 postnatal | Many regions | |||||||||||||||
87 | Developmental Dynamics of RNA Translation in the Human Brain | Nat Neuro, 2022 | Erin Duffy | Michael Greenberg | RNAseq, RiboSeq | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=9af49050&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Primary | |||||||||||||||||
88 | Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex | Nat Comm, 2023 | Iva 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, Mm | Primary | GW11-GW20 | ||||||||||||||||
89 | Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH | Nature, 2021 | Meng Zhang | Xiaowei Zhuang | MERFISH | Source | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=7e14ad94&gene_symbol_exact_match=1&gene_symbol=satb2 | Mm | Primary | Adult | MOp | |||||||||||||||
90 | Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer's disease | Genome Med, 2016 | Minghui Wang | Bin Zhang | Microarray | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=db52d017&gene_symbol_exact_match=1&gene_symbol=satb2 | Hs | Primary | Adult | |||||||||||||||||
91 | Dissecting neural differentiation regulatory networks through epigenetic footprinting | Nature, 2015 | Michael Ziller | Alexander Meissner | RNAseq | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2cfae2bd&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | 2D | ||||||||||||||||||
92 | Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors | Nat Commun, 2015 | Reuven Edri | Yechiel Elkabetz | Microarray | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=2cfae2bd&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | 2D | ||||||||||||||||||
93 | Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing | Nat Neuro, 2018 | Hannah Hochgerner | Sten Linnarsson | scRNAseq | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx | Mm | Primary | Adult | |||||||||||||||||
94 | Decoding the development of the human hippocampus | Nature 2020 | Suijuan Zhong | Xiaoqun Wang | scRNA-seq, scATACseq | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=d266f8be&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Primary | fetal: GW16–27 | |||||||||||||||||
95 | Spatiotemporal molecular dynamics of the developing human thalamus | Science, 2023 | Chang Kim | Tomasz Nowakowski | scRNAseq, MERFISH | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=b0019b85&gene_symbol_exact_match=1&gene_symbol=dcx | Hs | Primary | ||||||||||||||||||
96 | Conserved cell types with divergent features in human versus mouse cortex | Nature, 2019 | Rebecca Hodge | Ed Lein | smartSeq | https://nemoanalytics.org/index.html?multigene_plots=0&layout_id=0e5c2656&gene_symbol_exact_match=1&gene_symbol=dcx | Hs, Mm | Primary | MTG, layer dissections | |||||||||||||||||
97 | Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain | Nat Neuro, 2023 | Aritra Bhatacharjee | Yi Zhang | MERFISH | Source | Mm | primary | Adult | PFC | ||||||||||||||||
98 | ||||||||||||||||||||||||||
99 | ||||||||||||||||||||||||||
100 |