{"data":{"id":"10.6084/m9.figshare.654049","type":"dois","attributes":{"doi":"10.6084/m9.figshare.654049","prefix":"10.6084","suffix":"m9.figshare.654049","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Gavery, Mackenzie","nameType":"Personal","givenName":"Mackenzie","familyName":"Gavery","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Facilitating analysis of genomic variation in Olympia oysters"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"Marine Biology"},{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[],"dates":[{"date":"2013-03-18","dateType":"Created"},{"date":"2015-12-02","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["31766905 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (\u003cem\u003eOstrea lurida\u003c/em\u003e). The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format): \u003cstrong\u003eOly_snps_bed:\u003c/strong\u003e location of SNPs with variant annotated in the name column\u003cbr\u003e\u003cstrong\u003eOly_geneID_bed:\u003c/strong\u003e these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column\u003cbr\u003e\u003cstrong\u003eOly_regionofblasthits_bed:\u003c/strong\u003e these intervals cover only the region of homology between the subject and query for the blastx output\u003cbr\u003e\u003cstrong\u003eOly_inducible_bed:\u003c/strong\u003e these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: \u003cem\u003ecell-cell signaling, signal transduction, cell adhesion, development, stress response\u003c/em\u003e\u003cbr\u003e\u003cstrong\u003eOly_housekeeping_bed:\u003c/strong\u003e these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: \u003cem\u003eDNA metabolism, RNA metabolism, protein metabolism\u003c/em\u003e\u003cbr\u003e\u003cstrong\u003eOly_EcoRIsites_bed:\u003c/strong\u003e location of EcoRI restriction sites\u003cbr\u003e\u003cstrong\u003eOly_NotIsites_bed:\u003c/strong\u003e location of NotI restriction sites\u003cbr\u003e\u003cstrong\u003eOly_SbfI_bed:\u003c/strong\u003e location of SbfI restriction sites This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science. The slides for the final presentation are included (FISH546.pdf) The original data for the transcriptome, blastx annotations and SNP tables can be found here:\u003cbr\u003eTranscriptome characterization of the Olympia oyster and pinto abalone. Steven Roberts, Emma Timmins-Schiffman. figshare.\u003cbr\u003ehttp://dx.doi.org/10.6084/m9.figshare.156431. Retrieved 18:14, Mar 18, 2013 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