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Transposable element expression at unique loci in single cells with CELLO-seq

https://doi.org/10.1101/2020.10.02.322073
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What this work says

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

inferredcites →https://doi.org/10.1006/jmbi.1994.0095openalex-snapshot
Ancestral, Mammalian-wide Subfamilies of LINE-1 Repetitive Sequences
inferredcites →https://doi.org/10.1016/0168-9525(92)90262-3openalex-snapshot
Master genes in mammalian repetitive DNA amplification
inferredcites →https://doi.org/10.1016/j.cell.2010.10.019openalex-snapshot
Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome
inferredcites →https://doi.org/10.1016/j.cell.2012.04.019openalex-snapshot
Human Transposon Tectonics
inferredcites →https://doi.org/10.1016/j.cell.2018.05.043openalex-snapshot
A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity
inferredcites →https://doi.org/10.1016/j.stem.2017.10.004openalex-snapshot
An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.stemcr.2017.05.014openalex-snapshot
Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum
inferredcites →https://doi.org/10.1038/2413openalex-snapshot
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/550451aopenalex-snapshot
The Human Cell Atlas: from vision to reality
inferredcites →https://doi.org/10.1038/nature01262openalex-snapshot
Initial sequencing and comparative analysis of the mouse genome
inferredcites →https://doi.org/10.1038/nature11244openalex-snapshot
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
inferredcites →https://doi.org/10.1038/nature13760openalex-snapshot
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
inferredcites →https://doi.org/10.1038/nature21683openalex-snapshot
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
inferredcites →https://doi.org/10.1038/ncomms10286openalex-snapshot
Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells
inferredcites →https://doi.org/10.1038/ng.368openalex-snapshot
The regulated retrotransposon transcriptome of mammalian cells
inferredcites →https://doi.org/10.1038/ng.3945openalex-snapshot
LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo
inferredcites →https://doi.org/10.1038/nmeth.2639openalex-snapshot
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
inferredcites →https://doi.org/10.1038/nprot.2014.006openalex-snapshot
Full-length RNA-seq from single cells using Smart-seq2
inferredcites →https://doi.org/10.1038/nrg2072openalex-snapshot
Transposable elements and the epigenetic regulation of the genome
inferredcites →https://doi.org/10.1038/s41467-020-15171-6openalex-snapshot
Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
inferredcites →https://doi.org/10.1038/s41467-020-17800-6openalex-snapshot
High throughput error corrected Nanopore single cell transcriptome sequencing
inferredcites →https://doi.org/10.1038/s41586-019-0933-9openalex-snapshot
A single-cell molecular map of mouse gastrulation and early organogenesis
inferredcites →https://doi.org/10.1038/s41587-020-0570-8openalex-snapshot
A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity
inferredcites →https://doi.org/10.1038/s41592-019-0654-xopenalex-snapshot
Orchestrating single-cell analysis with Bioconductor
inferredcites →https://doi.org/10.1073/pnas.1607794113openalex-snapshot
Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing
inferredcites →https://doi.org/10.1073/pnas.1806447115openalex-snapshot
Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/dnares/dsw038openalex-snapshot
Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications
inferredcites →https://doi.org/10.1093/hmg/ddr455openalex-snapshot
Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility
inferredcites →https://doi.org/10.1093/nar/gku1001openalex-snapshot
DBTMEE: a database of transcriptome in mouse early embryos
inferredcites →https://doi.org/10.1093/nar/gkw928openalex-snapshot
The human-induced pluripotent stem cell initiative—data resources for cellular genetics
inferredcites →https://doi.org/10.1093/nar/gkz594openalex-snapshot
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes
inferredcites →https://doi.org/10.1101/085050openalex-snapshot
WhatsHap: fast and accurate read-based phasing
inferredcites →https://doi.org/10.1101/2020.04.06.027474openalex-snapshot
Combined single-cell gene and isoform expression analysis in haematopoietic stem and progenitor cells
inferredcites →https://doi.org/10.1101/462853openalex-snapshot
Single cell analysis reveals dynamics of transposable element transcription following epigenetic de-repression
inferredcites →https://doi.org/10.1101/645903openalex-snapshot
Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.177881.114openalex-snapshot
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
inferredcites →https://doi.org/10.1101/gr.190595.115openalex-snapshot
Defining cell types and states with single-cell genomics
inferredcites →https://doi.org/10.1101/gr.209601.116openalex-snapshot
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
inferredcites →https://doi.org/10.1128/jvi.02097-07openalex-snapshot
Murine Endogenous Retrovirus MuERV-L Is the Progenitor of the “Orphan” Epsilon Viruslike Particles of the Early Mouse Embryo
inferredcites →https://doi.org/10.1186/gb-2001-2-6-reviews1017openalex-snapshot
Endogenous retroviruses in the human genome sequence.
inferredcites →https://doi.org/10.1186/s12864-017-3566-0openalex-snapshot
Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
inferredcites →https://doi.org/10.1186/s13059-022-02615-zopenalex-snapshot
Single-cell isoform analysis in human immune cells
inferredcites →https://doi.org/10.1242/dev.132639openalex-snapshot
The impact of transposable elements on mammalian development
inferredcites →https://doi.org/10.1242/dev.167833openalex-snapshot
Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
inferredcites →https://doi.org/10.1534/g3.117.300257openalex-snapshot
Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol
inferredcites →https://doi.org/10.21105/joss.01316openalex-snapshot
Badread: simulation of error-prone long reads
inferredcites →https://doi.org/10.7554/elife.22345openalex-snapshot
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2022.02.09.479819openalex-snapshot
Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses
inferred← citeshttps://doi.org/10.3389/fcell.2022.854317openalex-snapshot
Single-Cell Multiomics Techniques: From Conception to Applications
inferred← citeshttps://doi.org/10.3390/cells10112952openalex-snapshot
The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation
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