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High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

https://doi.org/10.1083/jcb.202103078
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What this work says

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

inferredcites →https://doi.org/10.1002/0471142727.mb2129s109openalex-snapshot
ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
inferredcites →https://doi.org/10.1007/s10577-015-9509-1openalex-snapshot
ChIP bias as a function of cross-linking time
inferredcites →https://doi.org/10.1016/j.cell.2019.03.014openalex-snapshot
Profiling of Pluripotency Factors in Single Cells and Early Embryos
inferredcites →https://doi.org/10.1016/j.cell.2021.04.048openalex-snapshot
Integrated analysis of multimodal single-cell data
inferredcites →https://doi.org/10.1016/j.celrep.2012.08.003openalex-snapshot
CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
inferredcites →https://doi.org/10.1016/j.molcel.2015.11.003openalex-snapshot
A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes
inferredcites →https://doi.org/10.1016/j.molcel.2019.07.015openalex-snapshot
CoBATCH for High-Throughput Single-Cell Epigenomic Profiling
inferredcites →https://doi.org/10.1016/j.molcel.2021.09.019openalex-snapshot
Simultaneous profiling of multiple chromatin proteins in the same cells
inferredcites →https://doi.org/10.1038/nature19361openalex-snapshot
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
inferredcites →https://doi.org/10.1038/nbt.3652openalex-snapshot
Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution
inferredcites →https://doi.org/10.1038/nbt.4038openalex-snapshot
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
inferredcites →https://doi.org/10.1038/nbt.4112openalex-snapshot
Highly scalable generation of DNA methylation profiles in single cells
inferredcites →https://doi.org/10.1038/ncomms7033openalex-snapshot
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3488openalex-snapshot
A microfluidic device for epigenomic profiling using 100 cells
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/nprot.2011.345openalex-snapshot
Linear amplification for deep sequencing
inferredcites →https://doi.org/10.1038/nprot.2018.015openalex-snapshot
Targeted in situ genome-wide profiling with high efficiency for low cell numbers
inferredcites →https://doi.org/10.1038/s41467-019-09982-5openalex-snapshot
CUT&Tag for efficient epigenomic profiling of small samples and single cells
inferredcites →https://doi.org/10.1038/s41467-019-11559-1openalex-snapshot
Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)
inferredcites →https://doi.org/10.1038/s41467-019-13889-6openalex-snapshot
PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase
inferredcites →https://doi.org/10.1038/s41467-020-18309-8openalex-snapshot
Author Correction: Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)
inferredcites →https://doi.org/10.1038/s41556-018-0248-3openalex-snapshot
A chromatin integration labelling method enables epigenomic profiling with lower input
inferredcites →https://doi.org/10.1038/s41587-019-0147-6openalex-snapshot
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
inferredcites →https://doi.org/10.1038/s41587-019-0150-yopenalex-snapshot
Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells
inferredcites →https://doi.org/10.1038/s41587-021-00865-zopenalex-snapshot
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression
inferredcites →https://doi.org/10.1038/s41587-021-00869-9openalex-snapshot
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
inferredcites →https://doi.org/10.1038/s41587-022-01522-9openalex-snapshot
Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag
inferredcites →https://doi.org/10.1038/s41588-019-0424-9openalex-snapshot
High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
inferredcites →https://doi.org/10.1038/s41588-019-0429-4openalex-snapshot
Expanding the single-cell genomics toolkit
inferredcites →https://doi.org/10.1038/s41592-019-0361-7openalex-snapshot
Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
inferredcites →https://doi.org/10.1038/s41592-021-01060-3openalex-snapshot
Joint profiling of histone modifications and transcriptome in single cells from mouse brain
inferredcites →https://doi.org/10.1073/pnas.87.5.1663openalex-snapshot
Amplified RNA synthesized from limited quantities of heterogeneous cDNA.
inferredcites →https://doi.org/10.1073/pnas.89.7.3010openalex-snapshot
Analysis of gene expression in single live neurons.
inferredcites →https://doi.org/10.1074/jbc.m508013200openalex-snapshot
Extended Upstream A-T Sequence Increases T7 Promoter Strength
inferredcites →https://doi.org/10.1093/bfgp/ely012openalex-snapshot
A decade of ChIP-seq
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/gigascience/giab008openalex-snapshot
Twelve years of SAMtools and BCFtools
inferredcites →https://doi.org/10.1093/nar/gkm1144openalex-snapshot
Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification
inferredcites →https://doi.org/10.1093/nar/gkm891openalex-snapshot
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot
deepTools2: a next generation web server for deep-sequencing data analysis
inferredcites →https://doi.org/10.1101/2020.09.02.279703openalex-snapshot
Single-cell profiling of histone modifications in the mouse brain
inferredcites →https://doi.org/10.1101/2020.09.04.282418openalex-snapshot
Single-cell analysis of chromatin silencing programs in development and tumor progression
inferredcites →https://doi.org/10.1101/2021.04.27.441642openalex-snapshot
Simultaneous profiling of multiple chromatin proteins in the same cells
inferredcites →https://doi.org/10.1101/gr.260893.120openalex-snapshot
Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
inferredcites →https://doi.org/10.1126/science.aak9787openalex-snapshot
Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)
inferredcites →https://doi.org/10.1126/science.aam8940openalex-snapshot
Comprehensive single-cell transcriptional profiling of a multicellular organism
inferredcites →https://doi.org/10.1186/1471-2105-11-237openalex-snapshot
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s13059-016-0882-7openalex-snapshot
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
inferredcites →https://doi.org/10.1186/s13072-019-0287-4openalex-snapshot
Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
inferredcites →https://doi.org/10.1186/s13072-020-00343-xopenalex-snapshot
BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
inferredcites →https://doi.org/10.12688/f1000research.9037.1openalex-snapshot
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
inferredcites →https://doi.org/10.12688/f1000research.9037.2openalex-snapshot
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
inferredcites →https://doi.org/10.7554/elife.21856openalex-snapshot
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.4648584openalex-extracted
inferred← citeshttps://doi.org/10.1002/cpz1.535openalex-snapshot
FFPE‐ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin‐Fixed Paraffin‐Embedded Samples
inferred← citeshttps://doi.org/10.1002/ijc.35307openalex-snapshot
A hitchhiker's guide to single‐cell epigenomics: Methods and applications for cancer research
inferred← citeshttps://doi.org/10.1002/pro.4458openalex-snapshot
In situ tools for chromatin structural epigenomics
inferred← citeshttps://doi.org/10.1007/s11427-024-2770-xopenalex-snapshot
Advances and applications in single-cell and spatial genomics
inferred← citeshttps://doi.org/10.1016/j.cell.2022.09.035openalex-snapshot
Spatially resolved epigenomic profiling of single cells in complex tissues
inferred← citeshttps://doi.org/10.1016/j.cell.2022.10.014openalex-snapshot
Omics goes spatial epigenomics
inferred← citeshttps://doi.org/10.1016/j.molcel.2021.09.019openalex-snapshot
Simultaneous profiling of multiple chromatin proteins in the same cells
inferred← citeshttps://doi.org/10.1016/j.molcel.2023.06.018openalex-snapshot
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
inferred← citeshttps://doi.org/10.1016/j.trecan.2022.06.005openalex-snapshot
Single cell cancer epigenetics
inferred← citeshttps://doi.org/10.1021/jacs.4c01902openalex-snapshot
Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C-Terminal Domain Revealed by Chemical Synthesis
inferred← citeshttps://doi.org/10.1038/s41422-026-01275-zopenalex-snapshot
Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq
inferred← citeshttps://doi.org/10.1038/s41467-025-58137-2openalex-snapshot
CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks
inferred← citeshttps://doi.org/10.1038/s41467-026-73599-8openalex-snapshot
PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling
inferred← citeshttps://doi.org/10.1038/s41576-021-00407-yopenalex-snapshot
Epigenome plasticity in plants
inferred← citeshttps://doi.org/10.1038/s41576-022-00509-1openalex-snapshot
Characterizing cis-regulatory elements using single-cell epigenomics
inferred← citeshttps://doi.org/10.1038/s41587-022-01535-4openalex-snapshot
Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
inferred← citeshttps://doi.org/10.1038/s41592-023-01791-5openalex-snapshot
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry
inferred← citeshttps://doi.org/10.1038/s41594-023-00962-4openalex-snapshot
Replication licensing during S phase: breaking the law to prevent breaking DNA
inferred← citeshttps://doi.org/10.1038/s41596-023-00905-9openalex-snapshot
Scalable single-cell profiling of chromatin modifications with sciCUT&Tag
inferred← citeshttps://doi.org/10.1038/s41598-025-13316-5openalex-snapshot
NanoTag is an improved method to map interactions between DNA and proteins not requiring IgG
inferred← citeshttps://doi.org/10.1038/s43586-026-00491-6openalex-snapshot
Enzyme tethering for in situ epigenomics
inferred← citeshttps://doi.org/10.1080/15592294.2023.2293411openalex-snapshot
Cut&tag: a powerful epigenetic tool for chromatin profiling
inferred← citeshttps://doi.org/10.1093/bioadv/vbag023openalex-snapshot
MotifPeeker: benchmarking epigenomic profiling methods using motifs
inferred← citeshttps://doi.org/10.1093/nar/gkab813openalex-snapshot
FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
inferred← citeshttps://doi.org/10.1101/2021.04.27.441642openalex-snapshot
Simultaneous profiling of multiple chromatin proteins in the same cells
inferred← citeshttps://doi.org/10.1101/2023.01.15.524129openalex-snapshot
Thor-Ribo-Seq: ribosome profiling tailored for low input with RNA-dependent RNA amplification
inferred← citeshttps://doi.org/10.1101/2023.12.11.570452openalex-snapshot
Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development
inferred← citeshttps://doi.org/10.1101/2024.07.12.603224openalex-snapshot
NanoTag - an IgG-free method for mapping DNA-protein interactions
inferred← citeshttps://doi.org/10.1101/2024.10.08.617149openalex-snapshot
Rational design of peak calling parameters for TIP-seq based on pA-Tn5 insertion patterns improves predictive power
inferred← citeshttps://doi.org/10.1101/2025.08.06.668979openalex-snapshot
Ultra-parallel ribosome profiling platform with RNA-dependent RNA amplification
inferred← citeshttps://doi.org/10.1101/gr.275223.121openalex-snapshot
Tagmentation-based single-cell genomics
inferred← citeshttps://doi.org/10.1111/tpj.70403openalex-snapshot
Genome‐wide profiling the integration patterns with T7 ‐ PCR
inferred← citeshttps://doi.org/10.1126/sciadv.adu3308openalex-snapshot
Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq
inferred← citeshttps://doi.org/10.1177/11779322251365042openalex-snapshot
In Silico Separation of in Vitro Transcription-Derived Duplicates From PCR Duplicates to Enhance Sequence Data Utilization
inferred← citeshttps://doi.org/10.1186/s13059-025-03661-zopenalex-snapshot
IT-scC&T-seq streamlines scalable, parallel profiling of protein–DNA interactions in single cells
inferred← citeshttps://doi.org/10.1186/s13148-023-01574-xopenalex-snapshot
Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
inferred← citeshttps://doi.org/10.1242/dev.205059openalex-snapshot
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development
inferred← citeshttps://doi.org/10.1360/ssv-2025-0107openalex-snapshot
Advances and breakthroughs in single-cell nucleic acid omics
inferred← citeshttps://doi.org/10.15252/msb.202110571openalex-snapshot
Enablers and challenges of spatial omics, a melting pot of technologies
inferred← citeshttps://doi.org/10.20944/preprints202404.1213.v1openalex-snapshot
Harnessing Genetic Code: Futuristic Approach of Next-Generation Sequencing for Sustainable Future
inferred← citeshttps://doi.org/10.21105/joss.09672openalex-snapshot
nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets
inferred← citeshttps://doi.org/10.22541/au.169203623.39699591/v1openalex-snapshot
CUT&tag: A powerful epigenetic tool for chromatin profiling
inferred← citeshttps://doi.org/10.3390/genes16121394openalex-snapshot
A Single-Cell Omics Technical Guide for Advancing Neuropsychiatric Research
inferred← citeshttps://doi.org/10.3390/ijms232213984openalex-snapshot
2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells
inferred← citeshttps://doi.org/10.3390/mps6020024openalex-snapshot
Tn5 DNA Transposase in Multi-Omics Research
inferred← citeshttps://doi.org/10.64898/2025.12.04.692102openalex-snapshot
A single-nucleus multimodal framework reveals epigenomic priming of chemoresistant states in ovarian cancer
inferred← citeshttps://doi.org/10.64898/2026.03.26.714421openalex-snapshot
ECHOS enables spatial epigenome profiling at subcellular resolution
inferred← citeshttps://doi.org/10.64898/2026.06.21.732899openalex-snapshot
CREPAS: a reproducible nascent chromatin sequencing analysis pipeline for epigenome replication studies
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