ArticlePloS one2012
Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- Redefining clinical practice through spatial profiling: a revolution in tissue analysis.Annals of the Royal College of Surgeons of England · 2024Article
- Article
- Rapid and efficient enhancer cloning andSTAR protocols · 2021Article
- Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo.Developmental cell · 2019Article
- Developmental effector gene regulation: Multiplexed strategies for functional analysis.Developmental biology · 2019Article
- From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms.Genesis (New York, N.Y. : 2000) · 2018Review
- Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling.BMC genomics · 2018Article
- Eric Davidson: Steps to a gene regulatory network for development.Developmental biology · 2016Article
- A medium-scale assay for enhancer validation in amniotes.Developmental dynamics : an official publication of the American Association of Anatomists · 2015Article
- Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences.Genomics · 2015Review
- Response to Nodal morphogen gradient is determined by the kinetics of target gene induction.eLife · 2015Article
- Transcriptional enhancers: from properties to genome-wide predictions.Nature reviews. Genetics · 2014Review
- Experimental approaches for gene regulatory network construction: the chick as a model system.Genesis (New York, N.Y. : 2000) · 2013Review
- Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.Developmental biology · 2013Article
- Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown.Developmental biology · 2013Article
- Identifying transcriptional cis-regulatory modules in animal genomes.Wiley interdisciplinary reviews. Developmental biologyReview
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.