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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...a comparable signal-to-noise ratio between the two workflows. Using spa-ChIP-seq, we systematically evaluate multiple parameters including shearing and cross-linking conditions, buffer compositions, and the ratio of antibody to cell number. We find, for the first time to our knowledge, that weaker genomic...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...from the same research group, led by a pair of ASCL1 overexpression experiments (r = 0.95, 410/500 by up-regulated) (for GEO GSE153823, see Ali et al. 2020). As for ChIP-seq, experiments from different groups but comparable contexts showed elevated similarity, such as two experiments overexpressing...
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Method: Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
- Severin Berger,
- Mikhail Pachkov,
- Phil Arnold,
- Saeed Omidi,
- Nicholas Kelley,
- Silvia Salatino,
- and Erik van Nimwegen
Genome Res. July 2019 29: 1164-1177; Published in Advance May 28, 2019, doi:10.1101/gr.239319.118
...become a routine experimental approach for quantitatively characterizing the -wide binding of transcription factors (TFs), computational analysis procedures remain far from standardized, making it difficult to compare ChIP-seq results across experiments. In addition, although -wide binding patterns must...
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Method: Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
- Mingxiang Teng and
- Rafael A. Irizarry
Genome Res. November 2017 27: 1930-1938; Published in Advance October 12, 2017, doi:10.1101/gr.220673.117
...than running a peak caller and IDR (https://www.encodeproject.org/chip-seq/transcription_factor/). If we simply run SPP followed by IDR, the improvements of our algorithm are even larger, since this approach produced 29.5% of regions reported by only one laboratory (Supplemental Fig. S3C). Figure 4...
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Method: CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
- Daniel Savic,
- E. Christopher Partridge,
- Kimberly M. Newberry,
- Sophia B. Smith,
- Sarah K. Meadows,
- Brian S. Roberts,
- Mark Mackiewicz,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. October 2015 25: 1581-1589; Published in Advance September 9, 2015, doi:10.1101/gr.193540.115
...of the Flag antibody and our overall Flag epitope tagging approach.Moreover, our results suggest that future studies can utilize a simple PCR validation to screen cells prior to more extensive downstream experimentation (Western blot and ChIP-seq). We further compared our CETCh-seq data with standard ChIP-seq...
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Method: Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
- Peng Liu,
- Rajendran Sanalkumar,
- Emery H. Bresnick,
- Sündüz Keleş,
- and Colin N. Dewey
Genome Res. August 2016 26: 1124-1133; Published in Advance July 12, 2016, doi:10.1101/gr.199174.115
...to partition the training set into groups that have distinct RNA-seq read count distributions, and (2) the data set is informative for a large fraction of target genes. We find that Pol II ChIP-seq data meets both requirements. To examine the first requirement, we built a training set for human cell line K562...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...A prospective trial comparing programmable targeted long-read sequencing and short-read sequencing for genetic diagnosis of cerebellar ataxia Haloom Rafehi1,2,43, Liam G. Fearnley1,2,43, Justin Read3,4,43, Penny Snell3, Kayli C. Davies3,5, Liam Scott1, Greta Gillies3, Genevieve C. Thompson3,5, Tess...
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Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
- Antonio L.C. Gomes,
- Thomas Abeel,
- Matthew Peterson,
- Elham Azizi,
- Anna Lyubetskaya,
- Luís Carvalho,
- and James Galagan
Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
...representation are also shown (right). Cooperativity and site detection from ChIP-seq Genome Research 1689 www..org High-resolution binding site refinement We first applied our model to show its ability to detect a binding site at high resolution. In order to validate ourmodel, we compared it to a reference set...
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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
...the . The basic ChIP-seq procedure is outlined in Figure 1A, and detailed protocols (and data) from our two consortia can be obtained from the ENCODE and modENCODE production groups listed at the UCSC Genome Browser: http:// encodeproject.org/ENCODE/ and http://www.modencode.org/, respectively. Cells or tissues...
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Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...may direct stage-specific binding of UNC-62 to its targets: (1) differential use of the LIN-39 cofactor in specifying binding targets in Integrative ChIP-seq analysis in C. elegans Genome Research 945 www..org neurons compared with the intestine, and (2) binding to distinct DNA motifs by the UNC-62(7a...

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