ArticleBMC genomics2017
Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 54 citations in OpenAlex.
- A novelFrontiers in microbiology · 2026Article
- Isolation of a NovelMicroorganisms · 2025Article
- Mago nashi controls auxin-mediated embryo patterning in Arabidopsis by regulating transcript abundance.The New phytologist · 2025Article
- Epigenetic dynamics of partially methylated domains in human placenta and trophoblast stem cells.BMC genomics · 2024Article
- Article
- Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes.Life science alliance · 2024Article
- Influence of Heat Treatment on Tea Polyphenols and Their Impact on Improving Heat Tolerance inFoods (Basel, Switzerland) · 2023Article
- Transgenerational sperm DMRs escape DNA methylation erasure during embryonic development and epigenetic inheritance.Environmental epigenetics · 2023Article
- Post-bisulfite Adaptor Tagging Based on an ssDNA Ligation Technique (tPBAT).Methods in molecular biology (Clifton, N.J.) · 2023Article
- Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters.Nature cell biology · 2021Article
- The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes.PLoS genetics · 2021Article
- Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo.Nature communications · 2020Article
- Establishment of a novel cell cycle-related prognostic signature predicting prognosis in patients with endometrial cancer.Cancer cell international · 2020Article
- Nine glycolysis-related gene signature predicting the survival of patients with endometrial adenocarcinoma.Cancer cell international · 2020Article
- Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.Nucleic acids research · 2019Article
- Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome.GigaScience · 2019Article
- RNA Sequencing of Peripheral Blood Revealed that the Neurotropic TRK Receptor Signaling Pathway Shows Apparent Correlation in Recovery Following Spinal Cord Injury at Small Cohort.Journal of molecular neuroscience : MN · 2019Article
- Whole-genome bisulfite sequencing with improved accuracy and cost.Genome research · 2018Article
- Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.Genome biology · 2018Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMethylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored.
resultsWe have used the Illumina HiSeq platform for our PBAT-based WGBS, and found that different versions of HiSeq Control Software (HCS) and Real-Time Analysis (RTA) installed on the system provided different global CpG methylation levels (approximately 5% overall difference) for the same libraries. This problem was reproduced multiple times with different WGBS libraries and likely to be associated with the low sequence diversity of bisulfite-converted DNA. We found that HCS was the major determinant in the observed differences. To determine which version of HCS is most suitable for WGBS, we used substrates with predetermined CpG methylation levels, and found that HCS v2.0.5 is the best among the examined versions. HCS v2.0.12 showed the poorest performance and provided artificially lower CpG methylation levels when 5-methylcytosine is read as guanine (first read of PBAT-seq and second read of MethylC-seq). In addition, paired-end sequencing of low diversity libraries using HCS v2.2.38 or the latest HCS v2.2.58 was greatly affected by cluster densities.
conclusionsSoftware updates in the Illumina HiSeq platform can affect the outputs from low-diversity sequencing libraries such as WGBS libraries. More recent versions are not necessarily the better, and HCS v2.0.5 is currently the best for WGBS among the examined HCS versions. Thus, together with other experimental conditions, special care has to be taken on this point when CpG methylation levels are to be compared between different samples by WGBS.
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.