{"data":{"id":"10.6084/m9.figshare.1320987","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1320987","prefix":"10.6084","suffix":"m9.figshare.1320987","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Aimin Li","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"ALDB: a domestic-animal long noncoding RNA database"}],"publisher":"figshare","container":{},"publicationYear":2015,"subjects":[{"subject":"60114 Systems Biology","subjectScheme":"FOR"},{"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)"},{"subject":"Computational 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":"Biotechnology"}],"contributors":[],"dates":[{"date":"2015-03-03","dateType":"Created"},{"date":"2015-03-03","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["21714357 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":"\u003cstrong\u003eIntroduction\u003c/strong\u003e The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which we have identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities. \u003cstrong\u003eThis published compressed file(.zip) includes the following files:\u003c/strong\u003e\u003cstrong\u003e\u003cbr\u003e\u003c/strong\u003e \u003cstrong\u003ePig (Sus scrofa) lincRNAs\u003c/strong\u003e Pig lincRNAs (on SS_10.2 in GFF3 format)\u003cbr\u003e Pig lincRNAs (on SS_10.2 in GTF format)\u003cbr\u003e Pig lincRNAs (in fasta format) Pig lincRNAs (on SS_10.2 in GTF format) [Identified by Zhou et al. ] \u003cstrong\u003eChicken (Gallus gallus) lincRNAs\u003c/strong\u003e Chicken lincRNAs (on GG_4.0 in GFF3 format)\u003cbr\u003e Chicken lincRNAs (on GG_4.0 in GTF format)\u003cbr\u003e Chicken lincRNAs (in fasta format) \u003cstrong\u003eCow (Bos taurus) lincRNAs\u003c/strong\u003e Cow lincRNAs (on UMD_3.1 in GFF3 format)\u003cbr\u003e Cow lincRNAs (on UMD_3.1 in GTF format)\u003cbr\u003e Cow lincRNAs (in fasta format) \u003cstrong\u003ePig (Sus scrofa) expression\u003c/strong\u003e Pig FPKM expression levels, derived from ERA178851 using TopHat and Cufflinks\u003cbr\u003e Pig count expression levels, derived from ERA178851 using SummaryOverlaps \u003cstrong\u003eChicken (Gallus gallus) expression\u003c/strong\u003e Chicken FPKM expression levels, derived from SRA059960 using TopHat and Cufflinks\u003cbr\u003e Chicken count expression levels, derived from SRA059960 using SummaryOverlaps \u003cstrong\u003eCow (Bos taurus) expression\u003c/strong\u003e Cow FPKM expression levels, derived from SRA059960 using TopHat and Cufflinks\u003cbr\u003e Cow count expression levels, derived from SRA059960 using SummaryOverlaps \u003cstrong\u003eCNCI of lincRNA transcripts\u003c/strong\u003e ALDB_pig_lincRNAs_with_CNCI\u003cbr\u003e ALDB_chicken_lincRNAs_with_CNCI\u003cbr\u003e ALDB_cow_lincRNAs_with_CNCI","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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