all

The Animal Genome Size Database is a comprehensive catalog of animal genome size data created by Dr. T. Ryan Gregory. Access to the database is free and information is continually expanding. There are several ways to search the database. One can search by whole groups of animals, taxonomic classes, or by using the advanced search options using genus, species or common animal names. Search results are displayed in a customizable table or can be exported as an Excel spreadsheet. A link to site FAQ is provided, along with a list of references.

The CHORI-251 Chimpanzee BAC library has been constructed at the Children's Hospital Oakland Research Institute, BACPAC Resources, by Baoli Zhu for segments 1 and 2, Michael Nefedov for segments 3 and 4. DNA was isolated from white blood cells obtained from a male chimpanzee (Pan troglodytes, "Clint", Yerkes #C0471; birthdate: 6-6-80). Agarose embedded high molecular weight DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI Methylase for segments 1 and 2, and with MboI for segments 3 and 4. Size fractionated DNA was cloned into the pTARBAC2.1 vector between the EcoRI sites or pTARBAC1.3 vector between the BamHI sites. The ligation products were transformed into DH10B (T1 resistant) electrocompetent cells (BRL Life Technologies). The library has been arrayed into 384-well microtiter dishes and also gridded onto 24 22x22cm nylon high-density filter for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct Chimpanzee BAC clones, stamped in duplicate. BAC library construction was funded by a grant from NIH (#HG01165-06).

The CHORI-253 Sumatran Orangutan BAC library has been constructed by Michael Nefedov in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). Evan Eichler (Department of Genetics, Case Western Reserve University) facilitated contacts with Steve Taylor (Louisville Kentucky Zoo) to obtain a blood sample from a male Sumatran orangutan ("Segundo"). DNA was isolated from white blood cells by embedding the cells in agarose. Agarose embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI Methylase and the fragments were size-fractionated by pulsed-field gel electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were then transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library has been arrayed into 384-well microtiter dishes and also gridded onto eleven 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct Orangutan BAC clones, stamped in duplicate. Library characterization was performed by Qing Cao and Kazutoyo Osoegawa. This work was funded by NIH grant HG01165-06.

The CHORI-255 gorilla BAC library has been constructed by Michael Nefedov in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). To obtain DNA from this endangered species, a proposal was submitted by Evan Eichler (Case Western Reserve University, Cleveland) to the Species Survival Plan Coordinator (SSCP). After favorable review, Dr. Lisa Faust (the SSCP) kindly provided us a gorilla blood sample. This gorilla was a male Western lowland gorilla (“Frank”, #327, Gorilla gorilla gorilla) housed at the Lincoln Park Zoo (Chicago). High-molecular-weight DNA was isolated from white blood cells by embedding in agarose. The embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI Methylase and size fractionated by pulsed-field electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library has been arrayed into 576 “384-well” microtiter dishes and has subsequently been gridded onto twelve 22x22cm nylon high-density filters for probe hybridization screening. Each hybridization membrane represents over 18,000 distinct gorilla BAC clones (48 dishes), stamped in duplicate. Library characterization was performed by Qing Cao and Kazutoyo Osoegawa. BAC library construction was funded by NIH grants HG01165-07SI and HG025323-01 as part of the NIH-funded BAC Resource Network.

The CHORI-257 mouse lemur BAC library has been constructed by Michael Nefedov in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). Kidney was obtained from an adult female mouse lemur (Microcebus murinus) through John Allman, Division of Biology 216-76, Caltech, Pasadena, CA 91125. The local identification number for this animal is #8. A skin biopsy and a blood sample have been sent to the Coriell Cell Repositories to establish cell lines as part of the Integrated Primate Biomaterials and Information Resource (IPBIR) initiative. High-molecular-weight DNA was isolated from a kidney cell suspension prepared in a Dounce Homogenizer and the cells were embedded in agarose to stabilize the DNA. The embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase and size fractionated by pulsed-field electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library has been arrayed into 576 “384-well” microtiter dishes and also gridded onto twelve 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents about 18,000 distinct mouse lemur BAC clones, stamped in duplicate. Library characterization was performed by Qing Cao, Teresa Ren and Kazutoyo Osoegawa. This work was funded by NIH grant HG025323-01.

The CHORI-259 Common Marmoset (Callithrix jacchus, male) BAC library has been constructed in Pieter De Jong's Laboratory at the Children’s Hospital Oakland Research Institute, BACPAC Resources, by Doriana Misceo and Dr. Baoli Zhu using the cloning techniques developed in our laboratory (Osoegawa et al., 1998). The marmoset sample for this library waskindly provided by Dr.Suzette Tardif, Associate Director of the Southwest National Primate Research Center in San Antonio TX. DNA was isolated fromkidney cells obtained from a male marmoset(SNPRC #17081). Another sample from the same animal has been used to establish a permanent cell line which can be obtained from the IPBIR (Integrated Primate Biomaterials and Information Resource). Agarose-embedded high molecular weight DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase. Size fractionated DNA was ligated into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were transformed into DH10B (T1resistant) electrocompetent cells (Invitrogen). The library has been arrayed into 528 384-well microtiter dishes and alsogridded onto 11 22x22cm nylon high-densityfilter for screening by probe hybridization. Each hybridizationmembrane represents over 18,000 distinct BAC clones, stamped in duplicate. BAC library construction was funded by NIH grantsHG01165-07SI and HG025323-01 as part of the NIH-funded BAC Resource Network.

The CHORI-271 gibbon BAC Library has been constructed by Boudewijn ten Hallers and Baoli Zhu in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). DNA was isolated from blood from a wild-born Northern White-cheeked female “Asia” with international studbook #0098. The blood was kindly provided by Alan Mootnick, Director of the Gibbon Conservation Center (GCC), Santa Clarita, California. Blood samples were collected on May 18th 2004. High-molecular-weight DNA was isolated from white blood cells by embedding in 0.5% agarose gel. The embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase and size fractionated by pulsed-field electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library has been arrayed into 480 “384-well” microtiter dishes and has subsequently been gridded onto ten 22x22cm nylon high-density filters for probe hybridization screening. Each hybridization membrane represents over 18,000 distinct gibbon BAC clones (48 dishes), stamped in duplicate. Library characterization was performed by Teresa Ren and Dr. Kazutoyo Osoegawa. BAC library construction was funded by NIH grant HG025323-03 under the auspices of the NIH-funded BAC Resource Network.

The CHORI-273 Black Lemur (Eulemur macaco macaco) BAC library has been constructed by Boudewijn ten Hallers and Baoli Zhu in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The library preparation followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). Duke University Primate Center provided the kidney tissue from a female black lemur. (Additional data about the black lemur individual: Emm, Pandora II; DUPC ID# 6358 female; Date of Birth: 3/26/1990; Date of Death: 5/14/1997; Cause of death: euthanasia due to fibrosarcoma; Tissue obtained upon necropsy, and frozen at -80C in approximately 1 hour.) High-molecular-weight DNA was isolated from frozen kidney tissue and was embedded in agarose to stabilize the DNA. Agarose embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase and size fractionated by pulsed-field electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library will be arrayed into 576 (384-well) microtiter dishes and will subsequently be gridded onto twelve 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct BAC clones, stamped in duplicate. BAC library construction was funded as part of the NIH-funded BAC Resource Network by a grant from NIH.

The CHORI-277 Gorilla BAC Library has been generated by Baoli Zhu, in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The library preparation followed the general cloning approach developed in our laboratory Osoegawa et al., 1998. Blood from female gorilla “Kamilah” was kindly provided by Dr. Oliver Ryder from the Zoological Society of San Diego's center for Conservation and Research for Endangered Species (CRES). White blood cells were embedded in 0.5% InCert agarose and proteins were removed by a detergent/proteinaseK treatment. The resulting agarose-embedded high molecular weight DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase then size fractionated by pulsed-field gel electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pBACgmr vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electro-competent cells (Invitrogen). The library has been arrayed into 576, 384-well microtiter dishes and has subsequently been gridded onto 12, 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct BAC clones, stamped in duplicate. The preparation of this library was facilitated through a subcontract from the Sanger Institute, funded by The Wellcome Trust. The BAC library will be used as a key reagent for gorilla genome project. BAC-derived data will be co-assembled with whole-genome shotgun sequence data derived from small insert and fosmid libraries, each derived from the same gorilla "Kamilah". While the library is not currently in the public domain, it is expected that it will become publicly available in the near future.

This lemur BAC library was constructed by Ze Peng in the laboratory of Jan-Fang Cheng at Lawrence Berkeley National Laboratory using the genomic DNA isolated from a cell line of the ring-tailed lemur (Lemur catta, Coriell # AG07100C). Isolated DNA was partially digested with EcoRI and EcoRI methylase, size selected, and cloned into the pBACe3.6 vector according to the protocol described in Osoegawa et al. (1998). The ligated DNA was then transformed into DH10B electro-competent cells (Invitrogen 18290-015). This library contains 291 384-well plates with an average insert size of 174 Kb. The construction of this library was supported by a grant (HL66728-01) from the National Heart, Lung and Blood Institute of NIH.

A list of all nonhuman primate data sets available at the BAC Library of the Children's Hospital Oakland Research Institute (CHORI).

The RPCI-43 BAC Library has been constructed in our laboratory by Chung-Li Shu. DNA was isolated from white blood cells obtained from a male chimpanzee (Pan troglodytes, "Donald", blood collection date: 9-11-97). The blood sample from Donald (# CO551, birthdate: 10-15-1987) was obtained from the Yerkes Non-Human Primate Center in Atlanta, GA. The agarose-embedded DNA was partially digested with a combination of EcoRI and EcoRI Methylase. Size selected DNA was cloned into the pBACe3.6 vector between the EcoRI sites. The ligation products were transformed into DH10B electrocompetent cells (BRL Life Technologies). The library has been arrayed into 384-well microtiter dishes and also gridded onto 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct chimpanzee BAC clones, stamped in duplicate.

This website provides information about the Baboon Genome Project, which seeks to sequence the genome of the baboon (genus Papio). This site provides the preliminary draft assembly for download as contigs or scaffolds through a link to an FTP site. Additionally, traces are available through links from the NCBI Short Read Archive and the NCBI Trace Archive. Sequence reads are submitted to the NCBI Trace Archive or the Short Read Archive as they are produced. Assemblies of contigs and scaffolds (and BLAST access to data) will be made available on this site and in relevant public databases as they are produced.

This website provides information about the Gibbon Genome Project, which seeks to sequence the genome of the Northern white-cheeked gibbon (Nomascus leucogenys). The project is a collaboration between the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and the Genome Institute at Washington University. The project goal is to "produce a high quality draft genome assembly of the Northern white-cheeked gibbon from Sanger sequencing data from clones of different sizes, including small insert plasmids, BACs, and fosmids. The site includes access to version 1.0 of the assembly, and links to the BCM-HGSC FTP site and NCBI Trace Archive.

This website provides information about the Orangutan Genome Project, which sequenced the genome of the orangutan (Pongo pygmaeus). The sequencing project was a collaboration between the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and The Genome Institute at Washington University in St. Louis. The project produced a "WGS shotgun assembly, using a combination of small insert plasmids and large insert clone ends." Links to the final draft genome assembly and available sequence data (Sanger traces and transcript sequence) are provided on the website. Sequencing and comparative analysis of the orangutan genome were funded by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

This website provides information on the Sooty Mangabey Project, which seeks to sequence the genome of the sooty mangabey (Cercocebus atys). The goal of the genome sequencing project is to produce a high quality draft whole genome shotgun assembly. Funding for the sequencing and comparative analysis are provided by Guido Silvestri of the University of Pennsylvania and the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH). A link to the white paper is provided on the website. Sequence reads will be deposited in the NCBI Sequence Read Archive. Assemblies of contigs and scaffolds (and BLAST access to data) will be made available on this site and in relevant public databases as they are produced.

Pooled Genomic Indexing (PGI) is a method for mapping collections of Bacterial Artificial Chromosome (BAC) clones across species using a combination of clone pooling and DNA sequencing. PGI has been used to map a total of 16,495 unique rhesus BAC clones, gving 0.92X BAC clone coverage, to the positions of 18,035 homologous loci in the human genome NCBI Build 34. Approximately 57% of the human genome is covered by mapped BACs. A number of intrachromosomal rearrangements were detected by mapping multiple segments within the individual rhesus BACs onto multiple disjoint loci.

From the BioGRID website: The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 500,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 30 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.1 web interface contains new search and display features that enable rapid queries across multiple data types and sources. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.1 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin. All BioGRID documentation is available online in the BioGRID Wiki.

The initial goal of the chimpanzee genome sequencing project was to produce a draft sequence of a male chimpanzee (named Clint). The project was undertaken as a collaborative effort of the Broad Institute and the Washington University Genome Sequencing Center (WUGSC) and has been used for an initial comparison with the human genome. The project also produced a large collection of single-nucleotide polymorphisms (SNPs) within and between western and central chimpanzee populations, which provide a genetic backdrop for the study of human population genetics.

The Center for Structural Genomics of Infectious Diseases (CSGID) is a consortium of laboratories using state-of-the-art structural biology methods to determine the 3-D structures of proteins from major human pathogens. Laboratories participating in CSGID are: Northwestern University, University of Chicago, J. Craig Venter Institute, University College London, University of Virginia, UT Southwestern Medical Center at Dallas, and Washington University School of Medicine.

From the website of the Chinese Macaque SNP GBrowse: The Chinese Macaque SNP (CMSNP) database was developed by the Kunming Institute of Zoology (KIZ), the Beijing Genomics Institute at Shenzhen (BGI-Shenzhen), Chinese Academy of Sciences (CAS). The data is illustrated in GBrowse, which is developed under the GMOD database. Each SNP is annotated as CMSNP plus a number. The chromosomal distribution of the SNPs in Chinese macaque is displayed by the pie chart. As the first nonhuman primate genome-wide sequence variation database, the purpose of CMSNP is to organize and present the rhesus macaque sequence variation data, which is a useful resource for genomic and medical research.

The Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) is one of eight National Centers for Biomedical Computing (NCBC) and one of twelve inter-disciplinary Centers for Cancer Systems Biology (CCSB). MAGNet aims to "develop novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes." Tools developed by MAGNet are freely available to members of the research community.

The Department of Human Genetics at the Emory University School of Medicine focuses directly on human genetic disease, especially in neurogenetics, metabolic disease, and translational research. Information and links to research laboratories located in the Department are available on the website, as well as information for current clinical trials.

This webpage provides information and data for the current genome sequence assembly for the chimpanzee (Pan troglodytes). Links to download the chimpanzee genome sequence are provided through an FTP site. Previous assemblies of the gene sequence are also available.