%0 Journal Article %J Genome Res %D 2004 %T Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. %A Krzywinski, Martin %A Wallis, John %A Gösele, Claudia %A Bosdet, Ian %A Chiu, Readman %A Graves, Tina %A Hummel, Oliver %A Layman, Dan %A Mathewson, Carrie %A Wye, Natasja %A Zhu, Baoli %A Albracht, Derek %A Asano, Jennifer %A Barber, Sarah %A Brown-John, Mabel %A Chan, Susanna %A Chand, Steve %A Cloutier, Alison %A Davito, Jonathon %A Fjell, Chris %A Gaige, Tony %A Ganten, Detlev %A Girn, Noreen %A Guggenheimer, Kurtis %A Himmelbauer, Heinz %A Kreitler, Thomas %A Leach, Stephen %A Lee, Darlene %A Lehrach, Hans %A Mayo, Michael %A Mead, Kelly %A Olson, Teika %A Pandoh, Pawan %A Prabhu, Anna-Liisa %A Shin, Heesun %A Tänzer, Simone %A Thompson, Jason %A Tsai, Miranda %A Walker, Jason %A Yang, George %A Sekhon, Mandeep %A Hillier, LaDeana %A Zimdahl, Heike %A Marziali, Andre %A Osoegawa, Kazutoyo %A Zhao, Shaying %A Siddiqui, Asim %A De Jong, Pieter J %A Warren, Wes %A Mardis, Elaine %A McPherson, John D %A Wilson, Richard %A Hübner, Norbert %A Jones, Steven %A Marra, Marco %A Schein, Jacqueline %K Animals %K Automation %K Chromosomes %K Chromosomes, Artificial, Bacterial %K Chromosomes, Artificial, Yeast %K Cloning, Molecular %K Computational Biology %K Contig Mapping %K DNA Fingerprinting %K Genetic Markers %K Genome %K Physical Chromosome Mapping %K Polymerase Chain Reaction %K Rats %K Sequence Analysis, DNA %X

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

%B Genome Res %V 14 %P 766-79 %8 2004 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/15060021?dopt=Abstract %R 10.1101/gr.2336604 %0 Journal Article %J Biotechniques %D 2004 %T Large-scale RT-PCR recovery of full-length cDNA clones. %A Wu, Jia Qian %A Garcia, Angela M %A Hulyk, Steven %A Sneed, Anna %A Kowis, Carla %A Yuan, Ye %A Steffen, David %A McPherson, John D %A Gunaratne, Preethi H %A Richard A Gibbs %K Automation %K Cloning, Molecular %K DNA, Complementary %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Messenger %K Sequence Analysis, DNA %X

Pseudogenes, alternative transcripts, noncoding RNA, and polymorphisms each add extensive complexity to the mammalian transcriptome and confound estimation of the total number of genes. Despite advanced algorithms for gene prediction and several large-scale efforts to obtain cDNA clones for all human open reading frames (ORFs), no single collection is complete. To enhance this effort, we have developed a high-throughput pipeline for reverse transcription PCR (RT-PCR) gene recovery. Most importantly, novel molecular strategies for improving RT-PCR yield of transcripts that have been difficult to isolate by other means and computational strategies for clone sequence validation have been developed and optimized. This systematic gene recovery pipeline allows both rescue of predicted human and rat genes and provides insight into the complexity of the transcriptome through comparisons with existing data sets.

%B Biotechniques %V 36 %P 690-6, 698-700 %8 2004 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/15088387?dopt=Abstract %R 10.2144/04364DD03