RID source papers

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Joy, J et al.temp0000001 Show samples for pubmed id temp0000001Download annotation file for pubmed id temp0000001Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral-treatment initiationJCI2024Sites mapped hg38 by authors, LiftOver to hg19 by RID; hg38 chr1:143215526,chr14:104797,chr22:27857,chr10:38932016,chr11:51273823,chr20:28116956,chr9:44273175,chr20:29914512,chr16:36360872 not found in hg19
Munshi, M et al.temp0000002 Show samples for pubmed id temp0000002Download annotation file for pubmed id temp0000002Cleavage and Polyadenylation Specificity Factor 6 Regulates the Kinetics of HIV-1 Nuclear ImportCell report2023 
White, J et al.36602866 Show samples for pubmed id 36602866Download annotation file for pubmed id 36602866Clonally expanded HIV-1 proviruses with 5’-Leader defects can give rise to nonsuppressible residual viremiaJCI2023hg38 site chr1:522814417 not found in hg19, not entered in RID.
Einkauf, KB et al.35026153 Show samples for pubmed id 35026153Download annotation file for pubmed id 35026153Parallel analysis of transcription, integration, and sequence of single HIV-1 provirusesCell2022integration sites liftovered from hg38 to hg19. 27 sites were not found in hg19
Gao, S et al.36044447 Show samples for pubmed id 36044447Download annotation file for pubmed id 36044447HIV infected CD4+ T cell clones are more stable than uninfected clones during long-term antiretroviral therapyPlos Pathog.2022clone size counted based on sampling dates
Goubran, M et al.35632628 Show samples for pubmed id 35632628Download annotation file for pubmed id 35632628Isolation of a Human Betaretrovirus from Patients with Primary Biliary CholangitisViruses2022 
Katsuya, H et al.33844021 Show samples for pubmed id 33844021Download annotation file for pubmed id 33844021Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected IndividualsJID2022has both HIV1 and HTLV1
Sun, C et al.35347274 Show samples for pubmed id 35347274Download annotation file for pubmed id 35347274Droplet-microfluidics-assisted sequencing of HIV proviruses and their integration sites in cells from people on antiretroviral therapyNat Biomed Eng2022Sites LiftOver from hg38 to hg19
Bale, MJ et al.33832973 Show samples for pubmed id 33832973Download annotation file for pubmed id 33832973Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in ChildrenPLOS_pathog2021 
Brandt, LD et al.34202310 Show samples for pubmed id 34202310Download annotation file for pubmed id 34202310Tracking HIV-1 Infected Cell Clones Using Integration Site-Specific qPCRVirus2021 
Coffin, JM et al.33826675 Show samples for pubmed id 33826675Download annotation file for pubmed id 33826675Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapyPLOS_pathog2021Only a partial of integration sites have been entered in this dataset. The rest are in the datasets of other papers
Huang, AS et al.34636876 Show samples for pubmed id 34636876Download annotation file for pubmed id 34636876Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistenceJEM2021converted to hg19. Sample43 chr14:106728842 not in hg19
Patro, SC et al.34960744 Show samples for pubmed id 34960744Download annotation file for pubmed id 34960744New Approaches to Multi-Parametric HIV-1 Genetics Using Multiple Displacement Amplification: Determining the What, How, and Where of the HIV-1 ReservoirVirus2021 
Halvas, EK et al.33016926 Show samples for pubmed id 33016926Download annotation file for pubmed id 33016926HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virusJCI2020 
Yamakawa, T et al.33313334 Show samples for pubmed id 33313334Download annotation file for pubmed id 33313334A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/LymphomaMol Ther Methods Clin Dev2020 
Yoon, JK et al.33318172 Show samples for pubmed id 33318172Download annotation file for pubmed id 33318172HIV proviral DNA integration can drive T cell growth ex vivoPNAS2020 
Coffin, JM et al.31217357 Show samples for pubmed id 31217357Download annotation file for pubmed id 31217357Clones of infected cells arise early in HIV-infected individualsJCI Insight2019 
Einkauf, Kevin et al.30688658 Show samples for pubmed id 30688658Download annotation file for pubmed id 30688658Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapyJCI2019sites mapped to hg38 by authors, liftover to hg19 by RID. Patient2, site 21 not found in hg19
Ferris, AL et al.31291371 Show samples for pubmed id 31291371Download annotation file for pubmed id 31291371Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humansPLoS Pathog2019 
McManus, W et al.31361603 Show samples for pubmed id 31361603Download annotation file for pubmed id 31361603HIV-1 in Lymph Nodes is Maintained by Cellular Proliferation During ARTJCI2019 
Ode, H et al.30857886 Show samples for pubmed id 30857886Download annotation file for pubmed id 30857886dentifying integration sites of the HIV-1 genome with intact and aberrant ends through deep sequencingJ Virol Methods2019Patients P1 to P8 are the same as Maldarelli F. et. al., 2014, Science, 345:179-83; Table S2
Sharaf, R et al.30024859 Show samples for pubmed id 30024859Download annotation file for pubmed id 30024859HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollersJCI2019 
Artesi, M et al.28811663 Show samples for pubmed id 28811663Download annotation file for pubmed id 28811663Monitoring Molecular Response in Adult T-cell Leukemia/Lymphoma by High-Throughput Sequencing Clonality AnalysisLeukemia2017 
Cook, LB et al.24735963 Show samples for pubmed id 24735963Download annotation file for pubmed id 24735963The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemiaBlood2017 
Furuta, R et al.29186194 Show samples for pubmed id 29186194Download annotation file for pubmed id 29186194Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivoPLoS Pathog2017integration sites were mapped to hg38 by the authors. To make it consistent with RID, the sites have been converted to hg19. 137 sites were not found in hg19
Malhotra, S et al.29099869 Show samples for pubmed id 29099869Download annotation file for pubmed id 29099869Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomasPLoS Pathog.2017 
Romano, O et al.27095295 Show samples for pubmed id 27095295Download annotation file for pubmed id 27095295Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitmentSci Rep2016 
Sunshine, S et al.26912621 Show samples for pubmed id 26912621Download annotation file for pubmed id 26912621HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing AssayJV2016 
Singh, PK et al.26545813 Show samples for pubmed id 26545813Download annotation file for pubmed id 26545813LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genesGenes Dev2015 
Singh, PK et al.SRP065157 Show samples for pubmed id SRP065157Download annotation file for pubmed id SRP065157direct submission to Genbank SRP065157 by Parmit Kumar Singh, Andrea Ferris, Stephen H. Hughes and Henry L. LevinNA2015 
Wang, W et al.25521721 Show samples for pubmed id 25521721Download annotation file for pubmed id 25521721Frequent proviral integration of the human betaretrovirus in biliary epithelium of patients with autoimmune and idiopathic liver diseaseAliment Pharmacol Ther.2015 
De Ravin, SS et al.24501411 Show samples for pubmed id 24501411Download annotation file for pubmed id 24501411Enhancers are major targets for murine leukemia virus vector integrationJ Virol2014 
LaFave, MC et al.24464997 Show samples for pubmed id 24464997Download annotation file for pubmed id 24464997MLV integration site selection is driven by strong enhancers and active promotersNucleic Acids Res2014 
Maldarelli, Frank et al.24968937 Show samples for pubmed id 24968937Download annotation file for pubmed id 24968937Specific HIV integration sites are linked to clonal expansion and persistence of infected cellsScience2014 
Wagner, TA et al.25011556 Show samples for pubmed id 25011556Download annotation file for pubmed id 25011556HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infectionScience2014The samples of each patient were collected at several time points
Sherrill-Mix, S et al.23953889 Show samples for pubmed id 23953889Download annotation file for pubmed id 23953889HIV latency and integration site placement in five cell-based modelsRetrovirology2013 
Han, Y et al.15163705 Show samples for pubmed id 15163705Download annotation file for pubmed id 15163705Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genesJ Virol2010 
Ikeda, T et al.17262715 Show samples for pubmed id 17262715Download annotation file for pubmed id 17262715 Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapyJID2007 
Mack, KD et al.12843741 Show samples for pubmed id 12843741Download annotation file for pubmed id 12843741HIV insertions within and proximal to host cell genes are a common finding in tissues containing high levels of HIV DNA and macrophage-associated p24 antigen expressionJ Acquir Immune Defic Syndr2003 
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