Dataset Open Access
Jacqueline A. Robinson;
Saurabh Belsare;
Shifra Birnbaum;
Deborah E. Newman;
Jeannie Chan;
Jeremy P. Glenn;
Betsy Ferguson;
Laura A. Cox;
Jeffrey D. Wall
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nmm##2200000uu#4500</leader> <controlfield tag="005">20200124192617.0</controlfield> <controlfield tag="001">2583292</controlfield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">University of California, San Francisco</subfield> <subfield code="a">Saurabh Belsare</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Texas Biomedical Research Institute</subfield> <subfield code="a">Shifra Birnbaum</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Texas Biomedical Research Institute</subfield> <subfield code="a">Deborah E. Newman</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Texas Biomedical Research Institute</subfield> <subfield code="a">Jeannie Chan</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Texas Biomedical Research Institute</subfield> <subfield code="a">Jeremy P. Glenn</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Oregon National Primate Research Center</subfield> <subfield code="a">Betsy Ferguson</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Wake Forest School of Medicine</subfield> <subfield code="a">Laura A. Cox</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">University of California, San Francisco</subfield> <subfield code="a">Jeffrey D. Wall</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">4450</subfield> <subfield code="z">md5:1cf430bea88ddc96c590f30168805b1a</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_100_highcoverage_SNPRC_sample_info.txt</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">81579815</subfield> <subfield code="z">md5:d498ce3de7aeb911ec1f7669ebb0769d</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_24_olive_founders_phased.vcf.gz</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">1458021</subfield> <subfield code="z">md5:543c98281467c1eee636ad7f47dffc13</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_24_olive_founders_phased.vcf.gz.tbi</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">379832</subfield> <subfield code="z">md5:93ca92032ea155c78e8c941000bd8cae</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_AIMs_33founders_fixed_yellow_olive.txt</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">214608597</subfield> <subfield code="z">md5:3c81434aa167e07e10914f58890f7198</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_ldhelmet_recombination_maps.tar.gz</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">736815</subfield> <subfield code="z">md5:273612e6b708a217b072f3f5edaff7c3</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_LOF_mutations.txt</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">124695</subfield> <subfield code="z">md5:f7fc9de59189b31feb427b65867000cb</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/baboon_plink_ROH.bed</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">2981899</subfield> <subfield code="z">md5:e136c7c15ac3c8262e578af3178c6722</subfield> <subfield code="u">https://zenodo.org/record/2583292/files/Panu_2.0_Panu_3.0_chain_files.tar.gz</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2019-03-01</subfield> </datafield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="p">openaire_data</subfield> <subfield code="o">oai:zenodo.org:2583292</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="u">University of California, San Francisco</subfield> <subfield code="0">(orcid)0000-0002-5556-815X</subfield> <subfield code="a">Jacqueline A. Robinson</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">Resources for genomic analyses in baboons (genus Papio)</subfield> </datafield> <datafield tag="540" ind1=" " ind2=" "> <subfield code="u">https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode</subfield> <subfield code="a">Creative Commons Attribution Non Commercial No Derivatives 4.0 International</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a"><p>Resources for genomic analyses in baboons (genus <em>Papio</em>). See &quot;Analysis of 100 high coverage genomes from a pedigreed captive baboon colony&quot; by Robinson et al. 2019 for further details.</p> <p><strong>Panu_2.0_Panu_3.0_chain_files.tar.gz</strong> Chain files for converting coordinates between Panu_2.0 and Panu_3.0. All coordinates in the files below correspond to Panu_2.0, but can be converted to coordinates in the new assembly, Panu_3.0, using the chain files with liftOver (Hinrichs et al. 2006, DOI:10.1093/nar/gkj144).</p> <p><strong>baboon_100_highcoverage_SNPRC_sample_info.txt</strong> Sample information: Sample ID, Sequencing ID, Type, Sex, Fped (%), Admixed, Mean coverage (X). The type, sex, inbreeding coefficient (Fped), and admixture status are all based on the SNPRC pedigree.</p> <p><strong>baboon_24_olive_founders_phased.vcf.gz</strong> Phased VCF files for 24 olive baboon founders. Phasing was performed with Beagle (Browning and Browning 2007, DOI:10.1086/521987), assuming an effective population size of 40,000 individuals (Boissinot et al. 2014, DOI:10.1002/ajpa.22618). SNPs were filtered to remove singletons and thinned so that no two sites were closer than 10 bp. <strong>baboon_24_olive_founders_phased.vcf.gz.tbi</strong> is the index for the VCF file.</p> <p><br> <strong>baboon_ldhelmet_recombination_maps.tar.gz</strong> Fine-scale recombination maps produced with LDhelmet (Chan et al. 2012, DOI:10.1371/journal.pgen.1003090) based on phased genotypes from 24 olive baboon founders. Results from three block penalties are provided (5, 25, 50).</p> <p><strong>baboon_AIMs_33founders_fixed_yellow_olive.txt</strong> List of ancestry informative markers for distinguishing olive and yellow baboon ancestry. These sites represent fixed differences between 7 genetically yellow and 24 genetically olive baboons.</p> <p><strong>baboon_plink_ROH.bed</strong> Coordinates of runs of homozygosity in BED format, inferred with PLINK (Chang et al. 2015, DOI:10.1186/s13742-015-0047-8) using the default behavior of the --homozyg function. The following parameters were used to prune SNPs beforehand: --indep-pairwise 50 5 0.5. The columns are: chromosome, start position, end position, sample name.</p> <p><strong>baboon_LOF_mutations.txt</strong> List of putative LOF mutations annotated with SnpEff (Cingolani et al. 2012, DOI:10.4161/fly.19695). The following mutation types were included: &ldquo;stop_gained&rdquo;, &ldquo;start_lost&rdquo;, &ldquo;stop_lost&rdquo;, &ldquo;splice_acceptor_variant&rdquo;, &ldquo;splice_donor_variant&rdquo;.</p></subfield> </datafield> <datafield tag="773" ind1=" " ind2=" "> <subfield code="n">doi</subfield> <subfield code="i">isVersionOf</subfield> <subfield code="a">10.5281/zenodo.2583291</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.5281/zenodo.2583292</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">dataset</subfield> </datafield> </record>
All versions | This version | |
---|---|---|
Views | 366 | 366 |
Downloads | 168 | 168 |
Data volume | 8.6 GB | 8.6 GB |
Unique views | 315 | 315 |
Unique downloads | 89 | 89 |