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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...contributions from sequencing data of plasma cfDNA (Fig. 1). The individuals studied were participants who had undergone screening for NPC (Chan et al. 2017, 2023). These subjects underwent plasma EBV DNA testing by real-time polymerase chain reaction (PCR) for NPC screening. The screening trial was conducted...
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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...of every single gene including primer design and synthesis, PCR, gel purification, and sequencing. Particularly, construction of UAS-cDNA/ORF plasmids for long cDNAs or ORFs by the recombinational (Gateway) cloning technique is truly problematic. Therefore, the technical difficulties of construction...
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Method: A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission
- Mikhail Liskovykh,
- Nikolay V. Goncharov,
- Nikolai Petrov,
- Vasilisa Aksenova,
- Gianluca Pegoraro,
- Laurent L. Ozbun,
- William C. Reinhold,
- Sudhir Varma,
- Mary Dasso,
- Vadim Kumeiko,
- Hiroshi Masumoto,
- William C. Earnshaw,
- Vladimir Larionov,
- and Natalay Kouprina
Genome Res. October 2019 29: 1719-1732; Published in Advance September 12, 2019, doi:10.1101/gr.254276.119
...attempted to exclude that off-target effects might account for the most unexpected mitotic abnormalities induced by siRNA-mediated knockdown of these genes. We therefore ectopically expressed siRNA-resistant cDNAs encoding PINK1 and TRIO in RPE cells and tested their ability to rescue the knockdown...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...%) was in accordance with the RNA-seq data set (Fig. 2C; Supplemental Fig. S3A). We next performed qRT-PCR with cDNA derived from germ cells, Sertoli cells, and Leydig cells to detect the expression pattern of the 20 candidate lncRNAs and observed that six candidate lncRNAs (1700027A15Rik, 1700006J14Rik, 1700052I22Rik...
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RESOURCE: Sequence Evaluation of Four Pooled-Tissue Normalized Bovine cDNA Libraries and Construction of a Gene Index for Cattle
- Timothy P.L. Smith,
- William M. Grosse,
- Brad A. Freking,
- Andrew J. Roberts,
- Roger T. Stone,
- Eduardo Casas,
- James E. Wray,
- Joseph White,
- Jennifer Cho,
- Scott C. Fahrenkrug,
- Gary L. Bennett,
- Michael P. Heaton,
- William W. Laegreid,
- Gary A. Rohrer,
- Carol G. Chitko-McKown,
- Geo Pertea,
- Ingeborg Holt,
- Svetlana Karamycheva,
- Feng Liang,
- John Quackenbush,
- and John W. Keele
Genome Res. April 1, 2001 11: 626-630; doi:10.1101/gr.170101
.... ↵ Quackenbush J. , Liang F. , Holt I. , Pertea G. , Upton J. ( 2000 ) The TIGR Gene Indices: Reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28 : 141 – 145 . ↵ Smith T.P.L. , Godtel R.A. , Lee R.T. ( 2000 ) PCR-based reaction setup for high-throughput cDNA library sequencing...
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METHODS: Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes
- Piero Carninci,
- Yuko Shibata,
- Norihito Hayatsu,
- Yuichi Sugahara,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Hideaki Konno,
- Yasushi Okazaki,
- Masami Muramatsu,
- and Yoshihide Hayashizaki
Genome Res. October 1, 2000 10: 1617-1630; doi:10.1101/gr.145100
...created with PCR- and solid matrix–based technologies were only partially characterized and showed sequence redundancy similar to that of nonnormalized cDNA libraries used in ESTs projects. In addressing the normalization of full-length cDNAs, we felt that an aliquot of the mRNA initially used for the cDNA...
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METHODS: Screening of Gene-Associated Polymorphisms by Use of In-Gel Competitive Reassociation and EST (cDNA) Array Hybridization
- Koshichi Gotoh and
- Michio Oishi
Genome Res. March 1, 2003 13: 492-495; doi:10.1101/gr.434103
...Screening of Gene-Associated Polymorphisms by Use of In-Gel Competitive Reassociation and EST (cDNA) Array Hybridization Koshichi Gotoh 1 and Michio Oishi Human Gene 2, Kazusa DNA Research Institute, 2-6-7, Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan...
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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
.... Microdissection We prepared full-length libraries from small tissues, including 71 microdissected tissues (Tables 1 and 3 ). To this end, we modified the Cap-Trapper for small quantities of total RNA, without PCR, which might skew representation, especially at expanses of long cDNAs and would affect...
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RESOURCE: Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set
- Vincent VanBuren,
- Yulan Piao,
- Dawood B. Dudekula,
- Yong Qian,
- Mark G. Carter,
- Patrick R. Martin,
- Carole A. Stagg,
- Uwem C. Bassey,
- Kazuhiro Aiba,
- Toshio Hamatani,
- George J. Kargul,
- Amber G. Luo,
- Janet Kelso,
- Winston Hide,
- and Minoru S.H. Ko
Genome Res. December 1, 2002 12: 1999-2003; Published in Advance November 12, 2002, doi:10.1101/gr.633802
.... Trends Biotechnol. 19 : 511 – 518 . Piao Y. Ko N.T. Lim M.K. Ko M.S.H. ( 2001 ) Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Genome Res. 11 ( 9 ): 1553 – 1558 . Pruitt K.D. Maglott D.R. ( 2001 ) RefSeq and Locus...
ARTICLE: Panhandle PCR.
- D H Jones
Genome Res. April 1995 4: S195-S201
...tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification. Nucleic Acids Res. 19: 5227-5232. 9. Troutt, A.B., M.G. McHeyzer-Williams, B. Pulendran, and G.J.V. Nossal. 1992. Ligation-an- chored PCR: A simple amplification technique with single-sided specificity...
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