{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2500;ILLUMINA, Illumina Genome Analyzer IIx;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003992"],"sample_count":["64"],"description":["EGA dataset EGAD00001003992"],"repository":["EGA"],"title":["Human Pancreatic Beta Cell lncRNAs Control Cell-Specific Regulatory Networks - Whole Human Islet paired-ended RNA-seq assays"],"pubmed_abstract":["Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in human pancreatic β cells. β cell lncRNAs are often cell type specific and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role of lncRNAs in β cell gene regulation and diabetes, the function of β cell lncRNAs remains largely unknown. In this study, we investigated the function of β cell-specific lncRNAs and transcription factors using transcript knockdowns and co-expression network analysis. This revealed lncRNAs that function in concert with transcription factors to regulate β cell-specific transcriptional networks. We further demonstrate that the lncRNA PLUTO affects local 3D chromatin structure and transcription of PDX1, encoding a key β cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets from donors with type 2 diabetes or impaired glucose tolerance. These results implicate lncRNAs in the regulation of β cell-specific transcription factor networks."],"pubmed_title":["Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks."],"pubmed_authors":["Akerman Ildem I, Tu Zhidong Z, Beucher Anthony A, Rolando Delphine M Y DMY, Sauty-Colace Claire C, Benazra Marion M, Nakic Nikolina N, Yang Jialiang J, Wang Huan H, Pasquali Lorenzo L, Moran Ignasi I, Garcia-Hurtado Javier J, Castro Natalia N, Gonzalez-Franco Roser R, Stewart Andrew F AF, Bonner Caroline C, Piemonti Lorenzo L, Berney Thierry T, Groop Leif L, Kerr-Conte Julie J, Pattou Francois F, Argmann Carmen C, Schadt Eric E, Ravassard Philippe P, Ferrer Jorge J"],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, idiopathic CD4 positive T-lymphocytopenia, Data Set, IMD13, MENA, NDPP1, isocitrate lyase, ICL, l(2)02029, immunodeficiency 13, Enb, enb, ENA, Ena, CG15112, 2018., ENA/VASP, idiopathic Cd4 lymphopenia"],"description_synonyms":["Transplant Donor, human being, Man (Taxonomy), Organ Donor, Transplant Donors., Modern, Transplant, Tissue, Semen Donors, RNA-seq, human, Semen Donor, Human, Semen, Homo sapiens, Modern Man, Whole Transcriptome Shotgun Sequencing, Donor, Donors, Tissue Donor, Ovum Donor, Ovum, Ovum Donors, Organ Donors, Man, Organ"],"pubmed_title_synonyms":["Controlling, dTAF[[II]]230, TAF[[II]]250, d230, preventive therapy, human being, Modern, TAF200, l(3)84Ab, dTAFII250, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, prevention, Human, dTAF230, dmTAF[[II]]230, TAFII250, Homo sapiens, dmTAF1, Taf230, p230, TAF[[II]]250/230, TFIID, prevention and control, Man, TAF250, Taf[[II]]250, Taf200, dTAF[[II]]250, TAF[[II]]230, Man (Taxonomy), TFIID TAF250, reference sample, cel, cell, prophylaxis, Taf1p, TAF[II]250, CG17603, TAF[[II]], human, preventive measures, dTAF250, DmelCG17603, TAF1., Taf250, control, SR3-5, Modern Man, TAF, TAF230, Controlled, TAF1"],"pubmed_abstract_synonyms":["Modb1, Adult-Onset Diabetes Mellitus, Diabetes Type 2, type 2, T-cell leukemia, Materials, NMAN, Glukose, OPDX, AGL4, Monohydrate, Type 2 Diabetes Mellitus, (DL)-Isomer, diabetes mellitus type 2, Social Controls, dmTAF[[II]]230, Roles, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, Dextrose, Ipf1, IPF1, Concepts, Non-Insulin Dependent Diabetes Mellitus, Intolerance, Maturity Onset Diabetes, Leprb, PKCI1, Slow Onset, Formal Social Controls, Chromatins, DM - Diabetes mellitus, Man (Taxonomy), TFIID TAF250, PAGEN1, cel, long, Tissue, F10N7_150, Impaired Glucose Tolerances, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, DL-glucose, Ketosis-Resistant Diabetes Mellitus, NIDDM, Social, glucose, Noninsulin-Dependent, Diabetes mellitus, MODY (Maturity-onset diabetes of the young), Role Concepts, chromosome scaffold, AGAMOUS-like 4, zinc ion regulated proximal promoter sequence-specific DNA binding, Tissue Donor, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, transcription from bacterial-type RNA polymerase promoter, Non Insulin Dependent, TRANSCRIPTION FACTOR, db, RNA polymerase II distal enhancer sequence-specific binding, nuclear chromatin, AA673479, RNA polymerase II core promoter proximal region sequence-specific binding, dTAF[[II]]230, Hint, Transplant Donor, DM, Adult-onset diabetes mellitus, Modern, Ipk1, Transplant, TAF200, Semen Donors, TAFII-250, TAF250/230, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, INSDC_feature:misc_RNA, results, Noninsulin-dependent diabetes mellitus, OB-RGRP, Adult-Onset, TAFII250, Glucose Tolerance, HINT, Role Concept, Adult-Onset Diabetes, Role, Genetic Materials, NOS, AI481367, Donors, Ketosis Resistant, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, (alpha-D)-Isomer, Glucose Tolerances, Genetic Material, Maturity-Onset Diabetes Mellitus, PRKCNH1, F14P3.4, D-Glucose, Factors, STF-1, Control, F14P3_4, Type II Diabetes, INSDC_feature:gene, Type 2, Controls, Impaired, CG17603, TAF[[II]], GSF, cell_type, Transcription factor, human, Obr, Semen Donor, Diabetes NOS, Noninsulin-Dependent Diabetes Mellitus, type II, Semen, Decreased glucose tolerance, non-insulin-dependent, Non-Insulin Dependent Diabetes, Tolerance, Taf250, D Glucose, Material, SR3-5, Stf1, bacterial transcription, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, Cistron, IUF1, obl, Glucose Monohydrate, Regulation, metal ion regulated sequence-specific DNA binding, Ovum, Ovum Donors, Organ Donors, Slow-Onset, TAF230, metal ion regulated proximal promoter sequence-specific DNA binding, Regulations, gluco-hexose, T2DM - Type 2 Diabetes mellitus, cytoplasmic chromatin, d230, human being, conformation, Glucose, Noninsulin Dependent, PDX-1, Gene, dTAFII250, Idx1, SEPALLATA 2, DIABETES MELLITUS TYPE 02, EfW1, Transcription Factor, Maturity-onset diabetes, Human, IDX-1, zinc ion regulated core promoter proximal region sequence-specific DNA binding, Homo sapiens, dmTAF1, Taf230, Non-Insulin-Dependent, Diabetes mellitus (disorder), non-insulin-dependent diabetes mellitus, Man, Maturity-Onset Diabetes, TAF250, MODY4, T2DM, study, Taf200, Transcription, network topology analysis, dTAF[[II]]250, Genetic, cell, Mody4, Non-Insulin-Dependent Diabetes Mellitus, copper ion regulated core promoter proximal region sequence-specific binding., Glucose tolerance decreased, obese-like, Taf1p, Maturity Onset Diabetes Mellitus, adult-onset, Transplant Donors, dTAF250, Maturity-onset diabetes mellitus, Noninsulin Dependent Diabetes Mellitus, Stable, RNA polymerase II proximal promoter sequence-specific DNA binding, Diabetes Mellitus, copper ion regulated proximal promoter sequence-specific DNA binding, Ketosis-Resistant, Ovum Donor, TAF, Anhydrous, Diabetes, E3bp, E3BP, XlHbox-8, diabetes, proX, Organ, Adult Onset, Type 2 diabetes, Glucose Intolerances, TAF[[II]]250, (beta-D)-Isomer, Tolerances, Formal Social Control, Adult-onset diabetes, Type 2 diabetes mellitus, MODY, l(3)84Ab, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, BG:DS00004.13, function, Factor, Cistrons, Cell, dTAF230, Concept, diabetes mellitus (disease), transcription factor activity, Impaired Glucose Tolerance, T2D, Social Control, p230, Slow-Onset Diabetes Mellitus, Maturity-Onset, TAF[[II]]250/230, RNA polymerase II transcription factor activity, TFIID, Donor, Type 2 Diabetes Mellitus Non-Insulin Dependent, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, Taf[[II]]250, PKCI-1, LEPROT, ipf1, Type 2 Diabetes, TAF[[II]]230, Exhibit, IPF-1, diabetes mellitus, Organ Donor, Intolerances, TAF[II]250, metal ion regulated core promoter proximal region sequence-specific binding, copper ion regulated core promoter proximal region sequence-specific binding, F10N7.150, Anhydrous Dextrose, xlhbox8, Pkci, DmelCG17603, Pdx1, PDX1, Charon, DLDBP, Modern Man, Impaired Glucose, pdx-1, regulation, Type II, Stable Diabetes Mellitus, Maturity Onset, TAF1, Glc"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-ICL-01-03-2018-15:32:27:049-427 - samples","description":"Whole Human Islet paired-ended RNA-seq of 64 human pancreatic donors.","dates":{"updated":"2018-03-06 10:50:59"},"accession":"EGAD00001003992","cross_references":{"TAXONOMY":["9606"],"pubmed":["28041957"],"EGA":["EGAC00001000853","EGAS00001002865"]}}