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Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

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Molecular Identity of Human Outer Radial Glia during Cortical Development

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Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

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The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

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Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

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Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

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Chromatin Regulation by BAF170 Controls Cerebral Cortical Size and Thickness

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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

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Cerebral organoids model human brain development and microcephaly

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Dissecting neural differentiation regulatory networks through epigenetic footprinting

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Single-cell chromatin accessibility reveals principles of regulatory variation

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

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Highly scalable generation of DNA methylation profiles in single cells

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Dimensionality reduction for visualizing single-cell data using UMAP

inferredcites →https://doi.org/10.1038/nmeth.4031openalex-snapshot

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

inferredcites →https://doi.org/10.1038/nmeth.4150openalex-snapshot

Single-cell mRNA quantification and differential analysis with Census

inferredcites →https://doi.org/10.1038/nmeth.4154openalex-snapshot

Sequencing thousands of single-cell genomes with combinatorial indexing

inferredcites →https://doi.org/10.1038/nmeth.4155openalex-snapshot

Massively multiplex single-cell Hi-C

inferredcites →https://doi.org/10.1038/nmeth.4396openalex-snapshot

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

inferredcites →https://doi.org/10.1038/nmeth.4401openalex-snapshot

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

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Reversed graph embedding resolves complex single-cell trajectories

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Generation of cerebral organoids from human pluripotent stem cells

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Super-resolution microscopy with DNA-PAINT

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Generation of human brain region–specific organoids using a miniaturized spinning bioreactor

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Clathrin inhibitor Pitstop-2 disrupts the nuclear pore complex permeability barrier

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Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

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Fast and accurate short read alignment with Burrows–Wheeler transform

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Fast and accurate long-read alignment with Burrows–Wheeler transform

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BEDTools: a flexible suite of utilities for comparing genomic features

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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POU-III Transcription Factors (Brn1, Brn2, and Oct6) Influence Neurogenesis, Molecular Identity, and Migratory Destination of Upper-Layer Cells of the Cerebral Cortex

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GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

inferredcites →https://doi.org/10.1101/370346openalex-snapshot

Cis-topic modelling of single-cell epigenomes

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The accessible chromatin landscape of the hippocampus at single-cell resolution

inferredcites →https://doi.org/10.1101/gr.177881.114openalex-snapshot

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

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Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex

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Comprehensive single-cell transcriptional profiling of a multicellular organism

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Single-cell epigenomics: Recording the past and predicting the future

inferredcites →https://doi.org/10.1126/science.aap8809openalex-snapshot

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

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Transcriptome and epigenome landscape of human cortical development modeled in organoids

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Comprehensive functional genomic resource and integrative model for the human brain

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flowCore: a Bioconductor package for high throughput flow cytometry

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

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The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis

inferredcites →https://doi.org/10.3389/fnins.2018.00571openalex-snapshot

The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1

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A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s10577-019-09619-9openalex-snapshot

Genomic methods in profiling DNA accessibility and factor localization

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.06.012openalex-snapshot

Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation

inferred← citeshttps://doi.org/10.1038/s41588-024-01658-1openalex-snapshot

Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility

inferred← citeshttps://doi.org/10.1038/s41592-021-01060-3openalex-snapshot

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

inferred← citeshttps://doi.org/10.1038/s41594-019-0323-xopenalex-snapshot

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

inferred← citeshttps://doi.org/10.1038/s41596-022-00692-9openalex-snapshot

Chromatin accessibility profiling by ATAC-seq

inferred← citeshttps://doi.org/10.1042/bst20210128openalex-snapshot

Integration of functional genomics data to uncover cell type-specific pathways affected in Parkinson's disease

inferred← citeshttps://doi.org/10.1101/2020.06.26.173377openalex-snapshot

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos

inferred← citeshttps://doi.org/10.1101/2020.09.04.283887openalex-snapshot

TEA-seq: a trimodal assay for integrated single cell measurement of transcription, epitopes, and chromatin accessibility

inferred← citeshttps://doi.org/10.1186/s12864-023-09832-1openalex-snapshot

High-capacity sample multiplexing for single cell chromatin accessibility profiling

inferred← citeshttps://doi.org/10.3390/ijms22147612openalex-snapshot

Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits

inferred← citeshttps://doi.org/10.7554/elife.63632openalex-snapshot

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

inferred← citeshttps://doi.org/10.7554/elife.73971openalex-snapshot

Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads

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