ArticleNature protocols2014
Using TRIP for genome-wide position effect analysis in cultured cells.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 45 citations in OpenAlex.
- Systematic pegRNA design with PRIDICT2.0 and ePRIDICT for efficient prime editing.Nature protocols · 2026Review
- Polycomb repression works without Siesta, theScience advances · 2026Article
- Development of compact transcriptional effectors using high-throughput measurements in diverse contexts.Nature biotechnology · 2025Article
- Machine learning prediction of prime editing efficiency across diverse chromatin contexts.Nature biotechnology · 2025Article
- Using individual barcodes to increase quantification power of massively parallel reporter assays.BMC bioinformatics · 2025Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing.Nucleic acids research · 2024Article
- Widespread chromatin context-dependencies of DNA double-strand break repair proteins.Nature communications · 2024Article
- Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons.Molecular cell · 2023Article
- Systematic assays and resources for the functional annotation of non-coding variants.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2022Article
- Enhancer-gene specificity in development and disease.Development (Cambridge, England) · 2022Review
- Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.Molecular cell · 2021Article
- Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands.Nature communications · 2021Article
- MPRAdecoder: Processing of the Raw MPRA Data WithFrontiers in genetics · 2021Article
- De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome.PloS one · 2021Article
- Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair.Frontiers in genetics · 2021Article
- Local rewiring of genome-nuclear lamina interactions by transcription.The EMBO journal · 2020Article
- Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus.Nature microbiology · 2020Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line.
Indexed as
Identifiers
What OpenQuestion holds
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.