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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...explain the transcriptional regulation of your GOI, this does not mean that you have to do all of the “wet-laboratory” experiments yourself: Data mining is a crucial step in developing your hypotheses. Proliferation of easily accessible, large-scale, high-throughput studies provides fertile ground...
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LETTER: Characterizing Embryonic Gene Expression Patterns in the Mouse Using Nonredundant Sequence-Based Selection
- Rita Sousa-Nunes,
- Amer Ahmed Rana,
- Ross Kettleborough,
- Joshua M. Brickman,
- Melanie Clements,
- Alistair Forrest,
- Sean Grimmond,
- Philip Avner,
- James C. Smith,
- Sally L. Dunwoodie,
- and Rosa S.P. Beddington
Genome Res. December 2003 13: 2609-2620; Published in Advance January 1, 2003, doi:10.1101/gr.1362303
...Hybridization Mouse embryos were collected from CBA/Ca × C57Bl10or C57BL6 × C57BL6 matings at 6.5, 7.5, 8.5, and 9.5 dpc. Extra-embryonic membranes were removed in M2 medium ( Hogan et al. 1994 ) containing 10% fetal calf serum. Embryos were fixed overnight in 4% paraformaldehyde (PFA) in phosphate buffered...
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Resource: A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines
- David B. West,
- Ravi K. Pasumarthi,
- Brian Baridon,
- Esi Djan,
- Amanda Trainor,
- Stephen M. Griffey,
- Eric K. Engelhard,
- Jared Rapp,
- Bowen Li,
- Pieter J. de Jong,
- and K.C. Kent Lloyd
Genome Res. April 2015 25: 598-607; Published in Advance January 15, 2015, doi:10.1101/gr.184184.114
...to create a resource of gene-specific knockout embryonic stem (ES) cells for all protein-coding genes in the mouse . To date, this global cooperative project has produced sets of targeted and/or gene-trapped cell lines for ∼17,000 unique genes, primarily using ES cells derived from the C57BL/6N inbred mouse...
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LETTER: A General Approach for Identifying Distant Regulatory Elements Applied to the Gdf6 Gene
- Douglas P. Mortlock,
- Catherine Guenther,
- and David M. Kingsley
Genome Res. September 2003 13: 2069-2081; Published in Advance January 1, 2003, doi:10.1101/gr.1306003
...of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distant regulatory elements into smaller intervals for detailed study. The mouse Gdf6 gene is expressed in a number of distinct embryonic locations that are involved in the patterning of skeletal and soft...
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Resource: A piggyBac transposon-based genome-wide library of insertionally mutated Blm-deficient murine ES cells
- Wei Wang,
- Allan Bradley,
- and Yue Huang
Genome Res. April 2009 19: 667-673; Published in Advance February 20, 2009, doi:10.1101/gr.085621.108
.... ( 2008 ) Large-scale gene trapping in C57BL/6N mouse embryonic stem cells . Genome Res. 18 : 1670 – 1679 . ↵ Hom, C. , Hansen, J. , Schnütgen, F. , Seisenberger, C. , Floss, T. , Irgang, M. , De-Zolt, S. , Wurst, W. , von Melchner, H. , Noppinger, P.R. ( 2007 ) Splinkerette PCR for more efficient...
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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
...; Fitzgerald and Bateman 2004 ). In the same way, the that has been chosen for sequencing is the one of the C57BL/6 inbred strain, which is the most widely used strain, but it would not be surprising to discover in the end that different inbred strains in fact have a slightly different number of genes...
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Research: Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice
- Malte Spielmann,
- Naseebullah Kakar,
- Naeimeh Tayebi,
- Catherine Leettola,
- Gudrun Nürnberg,
- Nadine Sowada,
- Darío G. Lupiáñez,
- Izabela Harabula,
- Ricarda Flöttmann,
- Denise Horn,
- Wing Lee Chan,
- Lars Wittler,
- Rüstem Yilmaz,
- Janine Altmüller,
- Holger Thiele,
- Hans van Bokhoven,
- Charles E. Schwartz,
- Peter Nürnberg,
- James U. Bowie,
- Jamil Ahmad,
- Christian Kubisch,
- Stefan Mundlos,
- and Guntram Borck
Genome Res. February 2016 26: 183-191; Published in Advance January 11, 2016, doi:10.1101/gr.199430.115
...and Hadjantonakis 2011). All animal procedures were in accordance with institutional, state, and government regulations (Berlin: LAGeSo). ISH and skeletal preparations ISH for Zak, Fgf8, Trp63, and Shh was carried out on wild-type embryos (C57BL/6J) and mutant embryos at embryonic stages E11.5. Skeletal...
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ARTICLE: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- Piero Carninci,
- Kazunori Waki,
- Toshiyuki Shiraki,
- Hideaki Konno,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Katsunori Aizawa,
- Takahiro Arakawa,
- Yoshiyuki Ishii,
- Daisuke Sasaki,
- Hidemasa Bono,
- Shinji Kondo,
- Yuichi Sugahara,
- Rintaro Saito,
- Naoki Osato,
- Shiro Fukuda,
- Kenjiro Sato,
- Akira Watahiki,
- Tomoko Hirozane-Kishikawa,
- Mari Nakamura,
- Yuko Shibata,
- Ayako Yasunishi,
- Noriko Kikuchi,
- Atsushi Yoshiki,
- Moriaki Kusakabe,
- Stefano Gustincich,
- Kirk Beisel,
- William Pavan,
- Vassilis Aidinis,
- Akira Nakagawara,
- William A. Held,
- Hiroo Iwata,
- Tomohiro Kono,
- Hiromitsu Nakauchi,
- Paul Lyons,
- Christine Wells,
- David A. Hume,
- Michela Fagiolini,
- Takao K. Hensch,
- Michelle Brinkmeier,
- Sally Camper,
- Junji Hirota,
- Peter Mombaerts,
- Masami Muramatsu,
- Yasushi Okazaki,
- Jun Kawai,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703
...of any transcriptome, allowing us to identify the borders of the transcribed regions, and are, therefore, essential to describe the transcriptional units and transcriptional starting points and promoters. The majority of the libraries were derived from the strain C57Bl6/J, whose sequence has just became...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
....Cell culturemESCs were grown under standard serum conditions and passaged 1:10 every 2–3 d. Details are provided in the Supplemental Methods.Mouse strains and animal careAll mice were maintained on a C57BL/6J genetic background. Ago2flox/flox mice (B6.129P2(129S4)-Ago2tm1.1Tara/J) (O'Carroll et al. 2007) were...
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Research: PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX
- Erwan Delbarre,
- Kristina Ivanauskiene,
- Jane Spirkoski,
- Akshay Shah,
- Kristin Vekterud,
- Jan Øivind Moskaug,
- Stig Ove Bøe,
- Lee H. Wong,
- Thomas Küntziger,
- and Philippe Collas
Genome Res. June 2017 27: 913-921; Published in Advance March 24, 2017, doi:10.1101/gr.215830.116
...integrity in embryonic stem cells. Nucleic Acids Res 41: 4447–4458. Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP. 2013. Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP. J Cell Biol 201: 325–335. Cho S, Park JS, Kang YK. 2011. Dual functions...

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