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Embryonic gene transcription in the spiny mouse ( Acomys cahirinus ): an investigtion into the embryonic genome activation

https://doi.org/10.1101/280412
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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/(sici)1098-2795(199712)48:4<442::aid-mrd4>3.0.co;2-qopenalex-snapshot
Paternal transcripts for glucose-6-phosphate dehydrogenase and adenosine deaminase are first detectable in the human preimplantation embryo at the Three- to Four-Cell stage
inferredcites →https://doi.org/10.1002/0471142727.mb0419s103openalex-snapshot
Ribosomal RNA Depletion for Efficient Use of RNA‐Seq Capacity
inferredcites →https://doi.org/10.1002/bies.201100099openalex-snapshot
The evolution of menstruation: A new model for genetic assimilation
inferredcites →https://doi.org/10.1002/j.1460-2075.1982.tb01230.xopenalex-snapshot
The transition from maternal to embryonic control in the 2‐cell mouse embryo.
inferredcites →https://doi.org/10.1002/mrd.1080260113openalex-snapshot
Transition from maternal to embryonic control in early mammalian development: A comparison of several species
inferredcites →https://doi.org/10.1016/0012-1606(82)90325-6openalex-snapshot
Quantitative changes in total RNA, total poly(A), and ribosomes in early mouse embryos
inferredcites →https://doi.org/10.1016/j.ajog.2008.11.037openalex-snapshot
A role for menstruation in preconditioning the uterus for successful pregnancy
inferredcites →https://doi.org/10.1016/j.ajog.2016.07.041openalex-snapshot
First evidence of a menstruating rodent: the spiny mouse (Acomys cahirinus)
inferredcites →https://doi.org/10.1016/j.anireprosci.2014.05.016openalex-snapshot
Genome activation in bovine embryos: Review of the literature and new insights from RNA sequencing experiments
inferredcites →https://doi.org/10.1016/j.biocel.2004.12.001openalex-snapshot
O-GlcNAc glycosylation: a signal for the nuclear transport of cytosolic proteins?
inferredcites →https://doi.org/10.1016/j.cell.2016.12.026openalex-snapshot
Nuclear Localization of Mitochondrial TCA Cycle Enzymes as a Critical Step in Mammalian Zygotic Genome Activation
inferredcites →https://doi.org/10.1016/j.celrep.2013.12.030openalex-snapshot
The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species
inferredcites →https://doi.org/10.1016/j.jsbmb.2015.09.044openalex-snapshot
The feto-placental unit, and potential roles of dehydroepiandrosterone (DHEA) in prenatal and postnatal brain development: A re-examination using the spiny mouse
inferredcites →https://doi.org/10.1016/j.molcel.2017.08.003openalex-snapshot
The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence
inferredcites →https://doi.org/10.1016/j.theriogenology.2007.09.032openalex-snapshot
Virtues and limitations of the preimplantation mouse embryo as a model system
inferredcites →https://doi.org/10.1016/s0093-691x(97)00406-8openalex-snapshot
Temporal patterns of embryonic gene expression and their dependence on oogenetic factors
inferredcites →https://doi.org/10.1016/s1472-6483(10)60914-5openalex-snapshot
Real-time reverse transcription-polymerase chain reaction analysis of translation initiation factor 1A (eIF-1A) in human and mouse preimplantation embryos
inferredcites →https://doi.org/10.1017/s0967199400000861openalex-snapshot
Zygotic and embryonic gene expression in cow: a review of timing and mechanisms of early gene expression as compared with other species
inferredcites →https://doi.org/10.1017/s2040174417000368openalex-snapshot
Impact of the IVF laboratory environment on human preimplantation embryo phenotype
inferredcites →https://doi.org/10.1038/305331a0openalex-snapshot
Heat shock proteins, first major products of zygotic gene activity in mouse embryo
inferredcites →https://doi.org/10.1038/332459a0openalex-snapshot
Human gene expression first occurs between the four- and eight-cell stages of preimplantation development
inferredcites →https://doi.org/10.1038/nature03205openalex-snapshot
Regulation of cap-dependent translation by eIF4E inhibitory proteins
inferredcites →https://doi.org/10.1038/nature11499openalex-snapshot
Skin shedding and tissue regeneration in African spiny mice (Acomys)
inferredcites →https://doi.org/10.1038/nature12364openalex-snapshot
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
inferredcites →https://doi.org/10.1038/ncomms11164openalex-snapshot
Comparative analysis of ear-hole closure identifies epimorphic regeneration as a discrete trait in mammals
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1038/nrg1808openalex-snapshot
Roadmap to embryo implantation: clues from mouse models
inferredcites →https://doi.org/10.1038/nsmb.2660openalex-snapshot
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
inferredcites →https://doi.org/10.1038/s41598-017-09334-7openalex-snapshot
De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
inferredcites →https://doi.org/10.1071/rd06119openalex-snapshot
Temporal and spatial control of gene expression in early embryos of farm animals
inferredcites →https://doi.org/10.1071/rd07156openalex-snapshot
Cytoplasmic and nuclear determinants of the maternal-to-embryonic transition
inferredcites →https://doi.org/10.1071/rd12044openalex-snapshot
A superovulation protocol for the spiny mouse (Acomys cahirinus)
inferredcites →https://doi.org/10.1071/rd15504openalex-snapshot
Regulation of heat-inducible HSPA1A gene expression during maternal-to-embryo transition and in response to heat in in vitro-produced bovine embryos
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btw354openalex-snapshot
MultiQC: summarize analysis results for multiple tools and samples in a single report
inferredcites →https://doi.org/10.1093/biomet/35.3-4.246openalex-snapshot
THE TRANSFORMATION OF POISSON, BINOMIAL AND NEGATIVE-BINOMIAL DATA
inferredcites →https://doi.org/10.1093/hmg/ddh157openalex-snapshot
The unique transcriptome through day 3 of human preimplantation development
inferredcites →https://doi.org/10.1093/humrep/14.10.2544openalex-snapshot
A macaque model for studying mechanisms controlling oocyte development and maturation in human and non-human primates
inferredcites →https://doi.org/10.1093/molehr/gan063openalex-snapshot
Genomic RNA profiling and the programme controlling preimplantation mammalian development
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gks042openalex-snapshot
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
inferredcites →https://doi.org/10.1093/nar/gkv1309openalex-snapshot
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
inferredcites →https://doi.org/10.1101/033142openalex-snapshot
Sequenceserver: a modern graphical user interface for custom BLAST databases
inferredcites →https://doi.org/10.1101/gr.100594.109openalex-snapshot
Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
inferredcites →https://doi.org/10.1111/j.1742-4658.2010.07830.xopenalex-snapshot
Roles of heat shock factors in gametogenesis and development
inferredcites →https://doi.org/10.1126/science.1140693openalex-snapshot
The Maternal-Zygotic Transition: Death and Birth of RNAs
inferredcites →https://doi.org/10.1128/mcb.17.2.778openalex-snapshot
Evidence for the Involvement of Mouse Heat Shock Factor 1 in the Atypical Expression of the HSP70.1 Heat Shock Gene during Mouse Zygotic Genome Activation
inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot
A scaling normalization method for differential expression analysis of RNA-seq data
inferredcites →https://doi.org/10.1186/s12859-016-1457-zopenalex-snapshot
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
inferredcites →https://doi.org/10.1186/s12859-017-1714-9openalex-snapshot
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries
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/s12864-017-3827-yopenalex-snapshot
A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
inferredcites →https://doi.org/10.1186/s13059-014-0410-6openalex-snapshot
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
inferredcites →https://doi.org/10.1186/s13059-015-0702-5openalex-snapshot
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
inferredcites →https://doi.org/10.1186/s13742-015-0089-yopenalex-snapshot
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
inferredcites →https://doi.org/10.1210/en.2012-1953openalex-snapshot
Ontogeny of the Adrenal Gland in the Spiny Mouse, With Particular Reference to Production of the Steroids Cortisol and Dehydroepiandrosterone
inferredcites →https://doi.org/10.1210/en.2016-1877openalex-snapshot
The Endometrial Polarity Paradox: Differential Regulation of Polarity Within Secretory-Phase Human Endometrium
inferredcites →https://doi.org/10.1242/dev.033183openalex-snapshot
The maternal-to-zygotic transition: a play in two acts
inferredcites →https://doi.org/10.1242/dev.060426openalex-snapshot
Human pre-implantation embryo development
inferredcites →https://doi.org/10.1242/dev.064741openalex-snapshot
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development
inferredcites →https://doi.org/10.1242/dev.73.1.111openalex-snapshot
Control of events during early cleavage of the mouse embryo: an analysis of the ‘2-cell block’
inferredcites →https://doi.org/10.1242/jcs.175943openalex-snapshot
Embryo–epithelium interactions during implantation at a glance
inferredcites →https://doi.org/10.12688/f1000research.8987.2openalex-snapshot
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0153782openalex-snapshot
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
inferredcites →https://doi.org/10.1530/jrf.0.0820769openalex-snapshot
Control of protein synthesis during early cleavage of sheep embryos
inferredcites →https://doi.org/10.1530/jrf.0.0860637openalex-snapshot
Qualitative and quantitative changes in protein synthesis occur at the 8–16-cell stage of embryogenesis in the cow
inferredcites →https://doi.org/10.21105/joss.00257openalex-snapshot
Varistran: Anscombe's variance stabilizing transformation for RNA-seq gene expression data
inferredcites →https://doi.org/10.5281/zenodo.1165212openalex-snapshot
Topconfects R package
inferredcites →https://doi.org/10.7554/elife.24623openalex-snapshot
Macrophages are necessary for epimorphic regeneration in African spiny mice

What points at this work

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

inferred← citeshttps://doi.org/10.1186/s12915-022-01470-5openalex-snapshot
De novo emergence, existence, and demise of a protein-coding gene in murids
inferred← citeshttps://doi.org/10.1242/dev.167718openalex-snapshot
Model systems for regeneration: the spiny mouse, Acomys cahirinus
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.18034.1openalex-snapshot
Tumor suppressors inhibit reprogramming of African spiny mouse (Acomys) fibroblasts to induced pluripotent stem cells
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