ArticleGenome research2014
Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 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
99 citing papers in PubMed.
- Improved spike-in normalization clarifies the relationship between active histone modifications and transcription.Nature genetics · 2026Article
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.bioRxiv : the preprint server for biology · 2026Article
- Dual role of ZIC2 during neural induction: from priming transcription factor to enhancer activator.Nucleic acids research · 2026Article
- Hypoxic regulation of chromatin and gene transcription.Communications biology · 2026Article
- Polycomb repressive complexes 1 and 2 independently and dynamically regulate euchromatin during cerebellar neurodevelopment.PLoS genetics · 2025Article
- Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing.Cell reports methods · 2025Article
- Article
- Appropriate normalization is critical to improve reproducibility of tissue ChIP-seq.Serican journal of medicine · 2025Article
- RIF1 integrates DNA repair and transcriptional requirements during the establishment of humoral immune responses.Nature communications · 2025Article
- ChIP-Rx: Arabidopsis Chromatin Profiling Using Quantitative ChIP-Seq.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa.BMC genomics · 2024Article
- Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.Molecular cell · 2024Article
- A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression inbioRxiv : the preprint server for biology · 2024Article
- The Wild West of spike-in normalization.Nature biotechnology · 2024Article
- SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control.NAR genomics and bioinformatics · 2024Article
- Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.Nature genetics · 2024Article
- The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping.Briefings in bioinformatics · 2024Article
- Selective gene expression maintains human tRNA anticodon pools during differentiation.Nature cell biology · 2024Article
- Quantitative transcriptomic and epigenomic data analysis: a primer.Bioinformatics advances · 2024Review
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This "spike" chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.
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.