Literature DB >> 12466305

Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set.

Vincent VanBuren1, 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, Minoru S H Ko.   

Abstract

A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from embryonic and newborn organ libraries consisting of ~120,000 cDNA clones, which were initially re-arrayed into a set of ~11,000 unique cDNA clones. A set of tubes was constructed from the racks in this set to prevent contamination and potential mishandling errors in all further re-arrays. Sequences from this set (11K) were analyzed further for quality and clone identity, and high-quality clones with verified identity were re-arrayed into the final set (7.4K). The set is freely available, and a corresponding database was built to provide comprehensive annotation for those clones with known identity or homology, and has been made available through an extensive Web site that includes many link-outs to external databases and analysis servers.

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Year:  2002        PMID: 12466305      PMCID: PMC187561          DOI: 10.1101/gr.633802

Source DB:  PubMed          Journal:  Genome Res        ISSN: 1088-9051            Impact factor:   9.043


  10 in total

1.  RefSeq and LocusLink: NCBI gene-centered resources.

Authors:  K D Pruitt; D R Maglott
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  STACK: Sequence Tag Alignment and Consensus Knowledgebase.

Authors:  A Christoffels; A van Gelder; G Greyling; R Miller; T Hide; W Hide
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  Verification and initial annotation of the NIA mouse 15K cDNA clone set.

Authors:  G J Kargul; D B Dudekula; Y Qian; M K Lim; S A Jaradat; T S Tanaka; M G Carter; M S Ko
Journal:  Nat Genet       Date:  2001-05       Impact factor: 38.330

4.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

5.  Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray.

Authors:  T S Tanaka; S A Jaradat; M K Lim; G J Kargul; X Wang; M J Grahovac; S Pantano; Y Sano; Y Piao; R Nagaraja; H Doi; W H Wood; K G Becker; M S Ko
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-01       Impact factor: 11.205

Review 6.  Embryogenomics: developmental biology meets genomics.

Authors:  M S Ko
Journal:  Trends Biotechnol       Date:  2001-12       Impact factor: 19.536

7.  Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method.

Authors:  Y Piao; N T Ko; M K Lim; M S Ko
Journal:  Genome Res       Date:  2001-09       Impact factor: 9.043

8.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 9.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

10.  SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences.

Authors:  J M Hancock; J S Armstrong
Journal:  Comput Appl Biosci       Date:  1994-02
  10 in total
  20 in total

1.  High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization.

Authors:  Toshiyuki Yoshikawa; Yulan Piao; Jinhui Zhong; Ryo Matoba; Mark G Carter; Yuxia Wang; Ilya Goldberg; Minoru S H Ko
Journal:  Gene Expr Patterns       Date:  2005-12-01       Impact factor: 1.224

2.  Genes and pathways downstream of telomerase in melanoma metastasis.

Authors:  Sepideh Bagheri; Mehdi Nosrati; Shang Li; Sylvia Fong; Sima Torabian; Javier Rangel; Dan H Moore; Scot Federman; Rebecca R Laposa; Frederick L Baehner; Richard W Sagebiel; James E Cleaver; Christopher Haqq; Robert J Debs; Elizabeth H Blackburn; Mohammed Kashani-Sabet
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-17       Impact factor: 11.205

3.  Modern origin of numerous alternatively spliced human introns from tandem arrays.

Authors:  Degen Zhuo; Richard Madden; Sherif Abou Elela; Benoit Chabot
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-08       Impact factor: 11.205

4.  Deficient degradation of homotrimeric type I collagen, α1(I)3 glomerulopathy in oim mice.

Authors:  Anna M Roberts-Pilgrim; Elena Makareeva; Matthew H Myles; Cynthia L Besch-Williford; Amanda C Brodeur; Andrew L Walker; Sergey Leikin; Craig L Franklin; Charlotte L Phillips
Journal:  Mol Genet Metab       Date:  2011-07-31       Impact factor: 4.797

5.  An embryonic poly(A)-binding protein (ePAB) is expressed in mouse oocytes and early preimplantation embryos.

Authors:  Emre Seli; Maria D Lalioti; Sean M Flaherty; Denny Sakkas; Nihal Terzi; Joan A Steitz
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-03       Impact factor: 11.205

6.  Loss of TSLC1 causes male infertility due to a defect at the spermatid stage of spermatogenesis.

Authors:  Louise van der Weyden; Mark J Arends; Oriane E Chausiaux; Peter J Ellis; Ulrike C Lange; M Azim Surani; Nabeel Affara; Yoshinori Murakami; David J Adams; Allan Bradley
Journal:  Mol Cell Biol       Date:  2006-05       Impact factor: 4.272

7.  Requirement for Shh and Fox family genes at different stages in sweat gland development.

Authors:  Makoto Kunisada; Chang-Yi Cui; Yulan Piao; Minoru S H Ko; David Schlessinger
Journal:  Hum Mol Genet       Date:  2009-03-06       Impact factor: 6.150

8.  Global expression profiling identifies a novel biosignature for protein aggregation R120GCryAB cardiomyopathy in mice.

Authors:  Namakkal S Rajasekaran; Matthew A Firpo; Brett A Milash; Robert B Weiss; Ivor J Benjamin
Journal:  Physiol Genomics       Date:  2008-07-15       Impact factor: 3.107

9.  α-1,6-Fucosyltransferase (FUT8) inhibits hemoglobin production during differentiation of murine and K562 human erythroleukemia cells.

Authors:  Hitoshi Sasaki; Takanori Toda; Toru Furukawa; Yuki Mawatari; Rika Takaesu; Masashi Shimizu; Ryohei Wada; Dai Kato; Takahiko Utsugi; Masaya Ohtsu; Yasufumi Murakami
Journal:  J Biol Chem       Date:  2013-04-22       Impact factor: 5.157

Review 10.  Gene expression during the oocyte-to-embryo transition in mammals.

Authors:  Alexei V Evsikov; Caralina Marín de Evsikova
Journal:  Mol Reprod Dev       Date:  2009-09       Impact factor: 2.609

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