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Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
- Wanqing Shao and
- Ting Wang
Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
...development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type–specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression...
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Method: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
- Benjamin Kaminow,
- Sara Ballouz,
- Jesse Gillis,
- and Alexander Dobin
Genome Res. April 2022 32: 738-749; Published in Advance March 7, 2022, doi:10.1101/gr.275613.121
...that these results can be generalized for other types of functional sequencing assays, we calculated mapping error rates for the H3K4me3 histone modification ChIP-seq data set from the ENCODE consortium (Supplemental Fig. S37). Similar to the RNA-seq results, the error rate for reads overlapping homozygous variants...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
...expression. However, these investigations have relied on cap analysis of gene expression (CAGE), which captures only the 5′ end of a transcript, or have used time series of limited duration and resolution.Here, we aim to use high temporal resolution rRNA-depleted total RNA-seq measurements to capture...
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Method: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression
- Yipeng Gao,
- Lei Li,
- Christopher I. Amos,
- and Wei Li
Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
...of long 3′ UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. Cell 134: 175–187. doi:10.1016/j.cell.2008.05.045 ↵Bailey TL. 2011. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27: 1653–1659. doi:10.1093/bioinformatics/btr261 ↵Brennecke P...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
...genomic data, including high-quality assembly and annotation for sika deer, remain lacking. This gap, combined with the challenges of determining regulatory relationships between regulatory elements (REs) and target genes (TGs) using standard ATAC-seq and histone ChIP-seq methods, have greatly hindered...
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Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
- Hideya Kawaji,
- Marina Lizio,
- Masayoshi Itoh,
- Mutsumi Kanamori-Katayama,
- Ai Kaiho,
- Hiromi Nishiyori-Sueki,
- Jay W. Shin,
- Miki Kojima-Ishiyama,
- Mitsuoki Kawano,
- Mitsuyoshi Murata,
- Noriko Ninomiya-Fukuda,
- Sachi Ishikawa-Kato,
- Sayaka Nagao-Sato,
- Shohei Noma,
- Yoshihide Hayashizaki,
- Alistair R.R. Forrest,
- Piero Carninci,
- and The FANTOM Consortium
Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
...of the cases. For example, transcriptional initiation of SNAPC4 is far (1k–2k bp) upstream of the RefSeq and GENCODE gene model 59 ends (Fig. 3B). CAGE finds a peak upstream, which is supported by ChIP-seq for H3K27 acetylation performed by the ENCODE Project (Ram et al. 2011). Such inaccuracies of gene models...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...a minor impact on TSS identification and quantification (r = 0.77) (Supplemental Fig. S5D,F).csRNA-seq identifies changes in activity at regulatory elements with higher dynamic range and better correlation with neighboring gene transcription changes than assays such as ATAC-seq or H3K27ac ChIP-seq...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...
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Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
- Tsung-Cheng Chang,
- Mihaela Pertea,
- Sungyul Lee,
- Steven L. Salzberg,
- and Joshua T. Mendell
Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
...of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies...
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Method: Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
- Christopher M. Vockley,
- Cong Guo,
- William H. Majoros,
- Michael Nodzenski,
- Denise M. Scholtens,
- M. Geoffrey Hayes,
- William L. Lowe, Jr.,
- and Timothy E. Reddy
Genome Res. August 2015 25: 1206-1214; Published in Advance June 17, 2015, doi:10.1101/gr.190090.115
...(Creyghton et al. 2010). In ChIP-seq experiments performed on LCLs derived from five individuals heterozygous for rs73170828 (Kilpinen et al. 2013), there was substantially higher H3K27ac on the reference allele across the LCLs (P = 0.058, paired Wilcoxon test). Furthermore, there was an overall significant...

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