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Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
...guidelines used by ENCODE and modENCODE Genome Research 1817 www..org Replication, sequencing depth, library complexity, and site discovery Biological replicate experiments from independent cell cultures, embryo pools, or tissue samples are used to assess reproducibility. Initial RNA polymerase II ChIP-seq...
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Method: Identification of regulatory elements from nascent transcription using dREG
- Zhong Wang,
- Tinyi Chu,
- Lauren A. Choate,
- and Charles G. Danko
Genome Res. February 2019 29: 293-303; Published in Advance December 20, 2018, doi:10.1101/gr.238279.118
...polymerase initiation sites (Core et al. 2014). Regions identified by dREG were on average 6.4-fold shorter (460 bp for dREG sites) than H3K27ac ChIP-seq peaks (2924 bp on average), closer in size to high-resolution DNase-seq data (322 bp on average) (Fig. 2A). dREG frequently separated out individual TIRs...
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Method: Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins
- Haoyi Wang,
- David Mayhew,
- Xuhua Chen,
- Mark Johnston,
- and Robi David Mitra
Genome Res. May 2011 21: 748-755; Published in Advance April 6, 2011, doi:10.1101/gr.114850.110
...’’ each strain. Finally, Calling Card–seq is cost-effective: Calling Cards deposited by 10 to 20 yeast TFs can be identified on a single lane of an Illumina GAII flowcell. Multiplexing of the Calling Card–seq method is simpler and more economical than a multiplexed ChIP-seq experiment, because all TF...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...specific to one TF. (C) De novo motifs discovered in top-1000 ChIP-seq peaks (top) and central enrichment of these motifs in full consensus peak sets of Twi at 2–4 h, CTCF at 6–8 h, Mef2 at 6–8 h, Mef2 at 10–12 h, Bin at 6–8 h, and Bin at 10–12 h. (D) Overlaps among consensus peak sets for all TFs. (E...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...,919 peaks per sample in ATAC-seq mode (range: 15,420–238,210 peaks) and 51,838 peaks per sample in ChIP-seq mode (range: 14,594–201,757 peaks) (Supplemental Fig. S3; Supplemental Table S4). We merged ATAC-seq-mode and ChIP-seq-mode peaks separately across 104 samples following the method of Meuleman et al...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...epigenetic markersPreviously published (Shi et al. 2021a) ChIP-seq data for the H3K4me1 and H3K4me3 epigenetic marker were obtained from the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) (Barrett et al. 2013) under accession numbers GSM5379664 and GSM5379671, respectively. For each...
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Method: Sequence-based correction of barcode bias in massively parallel reporter assays
- Dongwon Lee,
- Ashish Kapoor,
- Changhee Lee,
- Michael Mudgett,
- Michael A. Beer,
- and Aravinda Chakravarti
Genome Res. September 2021 31: 1638-1645; Published in Advance July 20, 2021, doi:10.1101/gr.268599.120
..., but more careful evaluations are required. Ultimately, a sequence-based understanding of tag effects on reporter expression will help us to better interpret MPRA studies.Of note, the SVR with gkm-kernel is a generalizable approach and can be applied to other problems, such as quantitative prediction of ChIP-seq...
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Research: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
- Guillaume Andrey,
- Robert Schöpflin,
- Ivana Jerković,
- Verena Heinrich,
- Daniel M. Ibrahim,
- Christina Paliou,
- Myriam Hochradel,
- Bernd Timmermann,
- Stefan Haas,
- Martin Vingron,
- and Stefan Mundlos
Genome Res. February 2017 27: 223-233; Published in Advance December 6, 2016, doi:10.1101/gr.213066.116
...with an alternative approach, implemented in the software package CHiCAGO (Cairns Figure 1. Experimental setup and calling of interaction peaks. (A) Seven tissues were selected to perform CC, RNA-seq, and ChIP-seq from: fore- (FL) and hindlimb (HL) at E10.5, E11.5, and E13.5, as well as midbrain (MB) at E10.5. (B...
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Research: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
...candidate sequences were chosen on the basis of having ENCODE HepG2 ChIP-seq peaks for EP300 and H3K27ac marks. The candidates overlapped with or without ChIP-seq peaks for FOXA1, FOXA2, or HNF4A. Half the candidates overlapped with ChIP-seq peaks for RAD21, SMC3, and CHD2. In addition, the library included...
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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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