{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina Genome Analyzer II;, Illumina HiSeq 2000;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000425"],"sample_count":["568"],"description":["EGA dataset EGAD00001000425"],"repository":["EGA"],"title":["GENCORD2_RNAseq"],"pubmed_abstract":["DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression. DOI:http://dx.doi.org/10.7554/eLife.00523.001."],"pubmed_title":["Passive and active DNA methylation and the interplay with genetic variation in gene regulation."],"pubmed_authors":["Gutierrez-Arcelus Maria M, Lappalainen Tuuli T, Montgomery Stephen B SB, Buil Alfonso A, Ongen Halit H, Yurovsky Alisa A, Bryois Julien J, Giger Thomas T, Romano Luciana L, Planchon Alexandra A, Falconnet Emilie E, Bielser Deborah D, Gagnebin Maryline M, Padioleau Ismael I, Borel Christelle C, Letourneau Audrey A, Makrythanasis Periklis P, Guipponi Michel M, Gehrig Corinne C, Antonarakis Stylianos E SE, Dermitzakis Emmanouil T ET"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_title_synonyms":["Genetic Variations, Regulations, DNA methylation maintenance, Diversity, Materials, Genetic, Variations, Social Controls., Formal Social Control, Control, Gene, Diversities, INSDC_feature:gene, DNA Methylations, DNA methylation, Genetic Diversity, Controls, Cistrons, Social, Material, Social Control, Genetic Diversities, Genetic Materials, Cistron, regulation, DNA, Regulation, Methylations, Formal Social Controls, Methylation, Variation, Genetic Material"],"description_synonyms":["BamF, bim, biml, BamC, HCAP, bim-beta6, bam, RNA-seq, ham, BOD, alpha, CDLS3, fs(3)neo61, CG10422, BIM, Bam-C, BAM, BMH., Bam, SMC3L1, Whole Transcriptome Shotgun Sequencing, bim-beta7, bod, DmelCG10422, CSPG6, bimel"],"pubmed_abstract_synonyms":["MGC130048, Par1c, Materials, 2410041A17Rik, ACTG, ACTE, Gene Expression Profile, A4, DNA Methylations, Profiles, fs(1)M34, NK/GPI., DmelCG8201, csp2, Act5, Social Controls, l(1)G0420, DmelCG12051, dmTAF[[II]]230, School-Age, Roles, Associations, Concepts, HEL-176, Impacts, CG4601, Environmental Impacts, Gpi-1, Formal Social Controls, A, gamma sarcoglycan, C, DNA methylation maintenance, cyt5C, Man (Taxonomy), Gene Expressions, TFIID TAF250, DHO, cel, Nlk, CG18572, DNA methylation, Signatures, Epigenomic, Social, genetic, Environmental Impact, Expression Signature, act 42A, Role Concepts, Ac5C, Transcriptomes, CG4027, gamma-sarcoglycan, ACT, Act, CG16701, Gpi, dTAF[[II]]230, l(1)G0330, CG8201, Actin/BAP47, CTE-II, Modern, AACT, Expression Profiles, SG-gamma, familial, TAF200, CTE-IIa, act, dMARK, Ach1, hBACH, Diversities, ACH1, TAFII-250, TAF250/230, LACH1, CG11960, act42A, CG30131, CG30132, EMK, Gene Expression, GIG25, TAFII250, Role Concept, mOC-X, Su(b), Alpha-1-antichymotrypsin His-Pro-less, School Age, Expression Signatures, AFFX-Dros-ACTIN_M_r_at, GIG24, DPAR-1, Role, DFNA26, Genetic Materials, actin, sarcoglycan, NK|GPI, LACH, Expression Profile, GAT, DFNA20, Genetic Material, Transcriptome Profiles, Populations, Org, ORG, DmelCG4027, Drives, Epigenetic, l(1)G0117, Control, Gpi1-r, Actin, Gpi1-s, INSDC_feature:gene, Genetic Diversity, Controls, CG17603, gamma (35kDa dystrophin-associated glycoprotein), Gpi1-t, TAF[[II]], beta-actin/Bap47, human, l(1)G0486, l(1)G0245, l(2)27C1, actin5C, DMDA, l(1)G0009, Taf250, BcDNA:RH48823, Material, ACTL3, SR3-5, 35kD dystrophin-associated glycoprotein, Lach1, MARK, Cistron, inherited genetic, School-Age Population, DNA, Epigenetics, Regulation, BACH, Methylation, Bglap-rs1, TAF230, Gpi1s, l(1)Ab, Regulations, Act5c, d230, l(1)G0010, human being, SGCG_HUMAN, Transcriptome Profile, AI461847, Par-1c, ACT5C, Gene, CG12051, dTAFII250, Serpin A3, EfW1, Bach, TYPE, DOI, Human, DAGA4, l(1)G0025, Homo sapiens, dmTAF1, dPAR-1, Taf230, 35DAG, Cell growth-inhibiting gene 24|25 protein, Pgi, dPar-1, MAM, gamma-SG, SCG3, Man, TAF250, doi, study, School-Age Populations, 27C1, Taf200, act5C, Diversity, dTAF[[II]]250, Genetic, cell, Gpi-1r, l(2)k06323, Gpi-1s, Profile, BRWS2, Phi, Gpi-1t, Taf1p, Population, Expressions, fs(1)829, dTAF250, Act42a, anon-EST:fe2D2, PAR-1, 1700027G07Rik, DmelCG18572, Par-1, Expression, T11, School Age Population, TAF, constitutitional genetic, Act-5C, Methylations, Variation, Cte-II, Genetic Variations, l(1)G0177, 42A, par1, TAF[[II]]250, Transcriptome, CPS, Variations, 35 kDa dystrophin-associated glycoprotein, Formal Social Control, dJ393D12.2, dPAR1, dPar1, l(3)84Ab, BG:DS00004.13, MF, Cistrons, Amf, Cell, SGCG, LGMD2C, Concept, Impact, dTAF230, Environmental, CAD, Social Control, beta-actin, p230, anon-WO0210402.19, Gene Expression Signatures, Genetic Diversities, M32055, sequence, TAF[[II]]250/230, TFIID, Act42, Gene Expression Signature, methylation, ACTA3, NK, Taf[[II]]250, l(1)G0079, TAF[[II]]230, DMDA1, PYR1, VSCM, act 5C, TAF[II]250, School Age Populations, primary structure of sequence macromolecule, DmelCG17603, Gene Expression Profiles, Modern Man, SCARMD2, DPar1, Environments, DRORUD, regulation, BAP47, PAR1, Par1, ACTSG, Signature, hereditary, Bap47, Actin5C, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-GenCord2-22-05-2013-15:33:28:221-28 - samples","description":"GENCORD2 RNA-seq BAM files using BWA","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00001000425","cross_references":{"TAXONOMY":["9606"],"pubmed":["23755361"],"EGA":["EGAC00001000105","EGAS00001000446"]}}