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Retraction: Retraction Genome Res. September 2004 14: 1820

...genome;14/9/1820 1088-9051 Retraction Retraction Genome Research 12: 1860-1870 (2002) Domain Regulation of Imprinting Cluster in Kip2/Lit1 Subdomain on Mouse Chromosome 7F4/F5: Large-Scale DNA Methylation Analysis Reveals That DMR-Lit1 Is a Putative Imprinting Control Region Hitomi Yatsuki...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...and system limitations. Slightly retracting ROI boundaries within morphological borders improved the ability to capture region-specific gene expression.Using PCL-seq, we analyzed adjacent coronal sections of the mouse olfactory bulb. Structural features of the MCL and OPL were identified using DRAQ5 staining...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
..., reaching a maximum in extraembryonic tissues, and then retract in adulthood. This phenomenon is very well illustrated by the Igf2r locus, whose expansion to 10 Mb in the placenta brings six new genes, including the flanking genes Arid1b and Thbs2, under the control of the ICR, allowing their maternal...
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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...retracted (Venters and Pugh 2014). The main concerns raised were about the analyses of the core promoter elements downstream from the data acquisition (Siebert and Söding 2014), and in the retraction letter the investigators claim that to the best of their knowledge, the raw and processed ChIP-exo data...
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Research: Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
...neurite retraction (Mueller et al. 2005; Gu et al. 2014). The 3′ UTR of Rock1 contains conserved target sites to four miRNAs from the brain cluster: miR-218, miR-153, miR-135, and miR-124. When the WT reporter was transfected with the miR-ALL plasmid containing the four miRNAs, expression was repressed...
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Research: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
- Kasper D. Rasmussen,
- Ivan Berest,
- Sandra Keβler,
- Koutarou Nishimura,
- Lucía Simón-Carrasco,
- George S. Vassiliou,
- Marianne T. Pedersen,
- Jesper Christensen,
- Judith B. Zaugg,
- and Kristian Helin
Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118
...as input predicted TF binding sites defined by -wide PWM scanner (PWMscan) (Ambrosini et al. 2018) overlapped with the open regions from ATAC-seq. For the PWM database source, we used HOCOMOCO v10 database (Kulakovskiy et al. 2016), in which we replaced CDX4 and EVX1 motifs (that were retracted from...
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Method: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
...their database. The Capnocytophaga sp. oral taxon 329 has also been retracted from NCBI. Although removal of contaminated or incomplete s is warranted, the statistics provided by CheckM can help identify the problems associated with these s. In the case of Capnocytophaga sp. oral taxon 329, the CheckM statistics...
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LETTER: A Pneumatic Device for Rapid Loading of DNA Sequencing Gels
- Dimitrios A. Panussis,
- Mark W. Cook,
- Lisa L. Rifkin,
- Jacqueline E. Snider,
- Joseph T. Strong,
- Rebecca M. McGrane,
- Richard K. Wilson,
- and Elaine R. Mardis
Genome Res. May 1, 1998 8: 543-548; doi:10.1101/gr.8.5.543
...of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
..., and isobutylmethylxanthine) (Fig. 2B). As in MEFs, we observed that most IGs were minimally expressed during 3T3-L1 exponential growth and induced when cells reached confluence following contact inhibition (Fig. 2C). When quiescent 3T3-L1 cells were incubated with serum and IDX, the cells retracted and reentered the cell...
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